Starting phenix.real_space_refine on Sat Jul 4 18:10:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scz_25043/07_2026/7scz_25043.map" } resolution = 3.5 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= 0.006 sd= 0.073 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 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10435 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s 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: 23205 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1536 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 3.69, per 1000 atoms: 0.16 Number of scatterers: 23205 At special positions: 0 Unit cell: (89.46, 121.41, 120.345, 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 19 16.00 P 294 15.00 O 2959 8.00 N 2388 7.00 C 7110 6.00 H 10435 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: 3.36 Conformation dependent library (CDL) restraints added in 375.0 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 70.7% alpha, 3.9% beta 146 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.793A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.642A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.501A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 103 through 123 removed outlier: 3.644A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.633A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.142A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 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 122 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 433 through 439 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 457 through 465 removed outlier: 3.766A pdb=" N ASP K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.647A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.649A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.725A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 418 through 420 removed outlier: 6.351A pdb=" N CYS K 429 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 2390 1.07 - 1.26: 9404 1.26 - 1.45: 5394 1.45 - 1.63: 6804 1.63 - 1.82: 33 Bond restraints: 24025 Sorted by residual: bond pdb=" N LEU K 478 " pdb=" H LEU K 478 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER K 479 " pdb=" H SER K 479 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 DC J 69 " pdb=" H6 DC J 69 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG G 88 " pdb="HH11 ARG G 88 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC I -58 " pdb=" H6 DC I -58 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 24020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 43096 6.26 - 12.51: 483 12.51 - 18.77: 1 18.77 - 25.02: 0 25.02 - 31.28: 3 Bond angle restraints: 43583 Sorted by residual: angle pdb=" O5' DC I 70 " pdb=" C5' DC I 70 " pdb=" C4' DC I 70 " ideal model delta sigma weight residual 109.40 120.61 -11.21 8.00e-01 1.56e+00 1.96e+02 angle pdb=" O5' DG J -58 " pdb=" C5' DG J -58 " pdb=" C4' DG J -58 " ideal model delta sigma weight residual 109.40 119.54 -10.14 8.00e-01 1.56e+00 1.61e+02 angle pdb=" O5' DA I 16 " pdb=" C5' DA I 16 " pdb=" C4' DA I 16 " ideal model delta sigma weight residual 109.40 119.45 -10.05 8.00e-01 1.56e+00 1.58e+02 angle pdb=" O5' DT J -42 " pdb=" C5' DT J -42 " pdb=" C4' DT J -42 " ideal model delta sigma weight residual 109.40 119.12 -9.72 8.00e-01 1.56e+00 1.47e+02 angle pdb=" O5' DG I 20 " pdb=" C5' DG I 20 " pdb=" C4' DG I 20 " ideal model delta sigma weight residual 109.40 118.68 -9.28 8.00e-01 1.56e+00 1.34e+02 ... (remaining 43578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8370 35.32 - 70.64: 1611 70.64 - 105.96: 39 105.96 - 141.28: 1 141.28 - 176.60: 3 Dihedral angle restraints: 10024 sinusoidal: 7285 harmonic: 2739 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 141.32 -18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" CA SER K 431 " pdb=" C SER K 431 " pdb=" N THR K 432 " pdb=" CA THR K 432 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2096 0.163 - 0.326: 120 0.326 - 0.489: 15 0.489 - 0.652: 0 0.652 - 0.815: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.28 -0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 38 " -0.301 2.00e-02 2.50e+03 1.63e-01 7.98e+02 pdb=" N1 DT J 38 " -0.094 2.00e-02 2.50e+03 pdb=" C2 DT J 38 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DT J 38 " 0.285 2.00e-02 2.50e+03 pdb=" N3 DT J 38 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DT J 38 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT J 38 " -0.257 2.00e-02 2.50e+03 pdb=" C5 DT J 38 " 0.035 2.00e-02 2.50e+03 pdb=" C7 DT J 38 " 0.193 2.00e-02 2.50e+03 pdb=" C6 DT J 38 " 0.028 2.00e-02 2.50e+03 pdb=" H3 DT J 38 " 0.087 2.00e-02 2.50e+03 pdb=" H6 DT J 38 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.369 2.00e-02 2.50e+03 1.34e-01 6.26e+02 pdb=" N9 DG J 47 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.096 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.103 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.057 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.034 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.218 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.077 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.084 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.080 2.00e-02 2.50e+03 pdb=" H8 DG J 47 " 0.085 2.00e-02 2.50e+03 pdb=" H1 DG J 47 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 55 " 0.349 2.00e-02 2.50e+03 1.42e-01 6.07e+02 pdb=" N1 DT J 55 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 55 " -0.108 2.00e-02 2.50e+03 pdb=" O2 DT J 55 " -0.200 2.00e-02 2.50e+03 pdb=" N3 DT J 55 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DT J 55 " 0.045 2.00e-02 2.50e+03 pdb=" O4 DT J 55 " 0.211 2.00e-02 2.50e+03 pdb=" C5 DT J 55 " -0.050 2.00e-02 2.50e+03 pdb=" C7 DT J 55 " -0.093 2.00e-02 2.50e+03 pdb=" C6 DT J 55 " -0.064 2.00e-02 2.50e+03 pdb=" H3 DT J 55 " 0.035 2.00e-02 2.50e+03 pdb=" H6 DT J 55 " -0.059 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1155 2.18 - 2.79: 36628 2.79 - 3.39: 62947 3.39 - 4.00: 89620 4.00 - 4.60: 128365 Nonbonded interactions: 318715 Sorted by model distance: nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.578 2.450 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.617 2.450 nonbonded pdb=" OD2 ASP D 68 " pdb=" HH TYR F 98 " model vdw 1.621 2.450 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.628 2.450 ... (remaining 318710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 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: 1.060 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.120 Find NCS groups from input model: 0.180 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.014 0.065 13590 Z= 1.340 Angle : 1.917 13.497 19596 Z= 1.937 Chirality : 0.093 0.815 2232 Planarity : 0.035 0.172 1456 Dihedral : 27.439 176.605 5861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.13 % 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: 0.09 (0.26), residues: 832 helix: 0.25 (0.19), residues: 580 sheet: -0.58 (1.52), residues: 6 loop : -0.05 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 77 TYR 0.124 0.021 TYR C 57 PHE 0.049 0.012 PHE D 70 TRP 0.068 0.027 TRP K 481 HIS 0.014 0.004 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.01367 / 1.34 (13590) covalent geometry : angle 1.91699 / 1.94 (19596) hydrogen bonds : bond 0.13010 / 14.45 ( 818) hydrogen bonds : angle 6.36587 / 8.24 ( 2050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 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: A 108 ASN cc_start: 0.8343 (t0) cc_final: 0.8023 (t0) REVERT: B 98 TYR cc_start: 0.8484 (m-10) cc_final: 0.8270 (m-10) REVERT: C 40 SER cc_start: 0.7653 (p) cc_final: 0.7293 (p) REVERT: C 90 ASP cc_start: 0.6953 (t70) cc_final: 0.6674 (t70) REVERT: D 59 MET cc_start: 0.8395 (tpp) cc_final: 0.8195 (tpp) REVERT: D 89 ILE cc_start: 0.9266 (mt) cc_final: 0.8903 (mt) REVERT: E 97 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6935 (mt-10) REVERT: G 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.8059 (tp30) REVERT: H 88 THR cc_start: 0.9138 (m) cc_final: 0.8859 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3294 time to fit residues: 130.8885 Evaluate side-chains 196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN H 82 HIS K 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066055 restraints weight = 67564.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.069215 restraints weight = 23937.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071227 restraints weight = 14042.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072275 restraints weight = 10714.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072970 restraints weight = 9414.025| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13590 Z= 0.210 Angle : 0.861 7.840 19596 Z= 0.520 Chirality : 0.053 0.423 2232 Planarity : 0.007 0.069 1456 Dihedral : 31.681 179.417 4153 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.37 % Allowed : 12.01 % Favored : 85.61 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.27), residues: 832 helix: 1.41 (0.21), residues: 582 sheet: -1.67 (1.47), residues: 11 loop : -0.34 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.020 0.002 TYR C 57 PHE 0.029 0.002 PHE A 67 TRP 0.006 0.003 TRP K 481 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.21 (13590) covalent geometry : angle 0.86059 / 0.52 (19596) hydrogen bonds : bond 0.06723 / 7.64 ( 818) hydrogen bonds : angle 3.86581 / 4.82 ( 2050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7781 (tp30) cc_final: 0.7459 (tp30) REVERT: A 90 MET cc_start: 0.8175 (mmm) cc_final: 0.7935 (mmm) REVERT: B 77 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8934 (mtpp) REVERT: E 50 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8142 (tt0) REVERT: E 94 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7996 (tp30) REVERT: G 61 GLU cc_start: 0.8599 (tp30) cc_final: 0.8390 (tp30) REVERT: H 62 MET cc_start: 0.9143 (mmp) cc_final: 0.8708 (mmt) REVERT: H 68 ASP cc_start: 0.8411 (t0) cc_final: 0.8103 (t0) REVERT: K 409 LYS cc_start: 0.8249 (tttt) cc_final: 0.8001 (pttp) outliers start: 17 outliers final: 15 residues processed: 222 average time/residue: 0.2715 time to fit residues: 82.8100 Evaluate side-chains 213 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 446 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.063545 restraints weight = 68397.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066483 restraints weight = 24212.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068338 restraints weight = 14248.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069350 restraints weight = 10866.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069995 restraints weight = 9495.598| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13590 Z= 0.257 Angle : 0.768 8.629 19596 Z= 0.474 Chirality : 0.048 0.384 2232 Planarity : 0.005 0.047 1456 Dihedral : 31.677 177.093 4153 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.05 % Allowed : 13.27 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 832 helix: 1.80 (0.21), residues: 582 sheet: -1.75 (1.52), residues: 11 loop : -0.64 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.014 0.002 TYR F 98 PHE 0.021 0.002 PHE A 67 TRP 0.004 0.002 TRP K 481 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.26 (13590) covalent geometry : angle 0.76825 / 0.47 (19596) hydrogen bonds : bond 0.05764 / 6.53 ( 818) hydrogen bonds : angle 3.72428 / 4.66 ( 2050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7882 (tp30) cc_final: 0.7675 (tp30) REVERT: B 88 TYR cc_start: 0.8656 (m-10) cc_final: 0.7784 (m-10) REVERT: D 68 ASP cc_start: 0.8207 (t0) cc_final: 0.7964 (t0) REVERT: E 50 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8334 (tt0) REVERT: E 73 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 94 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7827 (tp30) REVERT: E 125 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8377 (mm-40) REVERT: F 25 ASN cc_start: 0.8558 (m110) cc_final: 0.8275 (m110) REVERT: G 92 GLU cc_start: 0.8772 (mp0) cc_final: 0.8505 (mp0) REVERT: G 104 GLN cc_start: 0.8270 (mm110) cc_final: 0.8017 (mm-40) REVERT: K 409 LYS cc_start: 0.8228 (tttt) cc_final: 0.7970 (pttp) REVERT: K 459 LEU cc_start: 0.8335 (tp) cc_final: 0.7975 (tp) outliers start: 29 outliers final: 26 residues processed: 211 average time/residue: 0.2579 time to fit residues: 76.0207 Evaluate side-chains 212 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063634 restraints weight = 68339.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066608 restraints weight = 24728.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068471 restraints weight = 14644.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069481 restraints weight = 11241.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070111 restraints weight = 9863.666| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13590 Z= 0.205 Angle : 0.698 7.754 19596 Z= 0.433 Chirality : 0.044 0.370 2232 Planarity : 0.004 0.046 1456 Dihedral : 31.640 173.093 4153 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.63 % Allowed : 15.08 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.28), residues: 832 helix: 2.07 (0.21), residues: 582 sheet: -1.72 (1.52), residues: 11 loop : -0.65 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.017 0.002 TYR H 83 PHE 0.013 0.001 PHE A 67 TRP 0.003 0.001 TRP K 481 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.21 (13590) covalent geometry : angle 0.69794 / 0.43 (19596) hydrogen bonds : bond 0.04826 / 5.45 ( 818) hydrogen bonds : angle 3.50316 / 4.36 ( 2050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.507 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: D 35 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7149 (mt-10) REVERT: D 68 ASP cc_start: 0.8112 (t0) cc_final: 0.7909 (t0) REVERT: E 50 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8355 (tt0) REVERT: E 94 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7801 (tp30) REVERT: E 125 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8402 (mm-40) REVERT: F 25 ASN cc_start: 0.8534 (m110) cc_final: 0.8266 (m110) REVERT: G 92 GLU cc_start: 0.8804 (mp0) cc_final: 0.8460 (mp0) REVERT: G 104 GLN cc_start: 0.8285 (mm110) cc_final: 0.7957 (mm110) REVERT: H 68 ASP cc_start: 0.8651 (t0) cc_final: 0.8314 (t0) REVERT: K 409 LYS cc_start: 0.8221 (tttt) cc_final: 0.7985 (pttp) outliers start: 26 outliers final: 25 residues processed: 206 average time/residue: 0.2534 time to fit residues: 72.3410 Evaluate side-chains 214 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.064197 restraints weight = 67767.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067133 restraints weight = 23923.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068979 restraints weight = 14073.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070005 restraints weight = 10768.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070533 restraints weight = 9412.056| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13590 Z= 0.183 Angle : 0.664 8.463 19596 Z= 0.416 Chirality : 0.043 0.367 2232 Planarity : 0.004 0.049 1456 Dihedral : 31.557 171.926 4153 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.19 % Allowed : 15.64 % Favored : 80.17 % 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: 2.15 (0.28), residues: 832 helix: 2.27 (0.21), residues: 582 sheet: -1.88 (1.44), residues: 11 loop : -0.54 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 452 TYR 0.013 0.001 TYR G 57 PHE 0.013 0.001 PHE A 67 TRP 0.004 0.001 TRP K 481 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (13590) covalent geometry : angle 0.66436 / 0.42 (19596) hydrogen bonds : bond 0.04467 / 5.04 ( 818) hydrogen bonds : angle 3.32508 / 4.16 ( 2050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.597 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: B 74 GLU cc_start: 0.8910 (tt0) cc_final: 0.8465 (mt-10) REVERT: D 35 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7140 (mt-10) REVERT: D 68 ASP cc_start: 0.8154 (t0) cc_final: 0.7943 (t0) REVERT: E 94 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8021 (tp30) REVERT: E 125 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8440 (mm-40) REVERT: F 25 ASN cc_start: 0.8446 (m110) cc_final: 0.8229 (m110) REVERT: G 61 GLU cc_start: 0.8497 (tp30) cc_final: 0.8279 (tp30) REVERT: G 92 GLU cc_start: 0.8855 (mp0) cc_final: 0.8494 (mp0) REVERT: G 104 GLN cc_start: 0.8359 (mm110) cc_final: 0.7991 (mm110) REVERT: H 68 ASP cc_start: 0.8681 (t0) cc_final: 0.8355 (t0) REVERT: H 93 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: K 409 LYS cc_start: 0.8282 (tttt) cc_final: 0.8040 (pttp) outliers start: 30 outliers final: 25 residues processed: 203 average time/residue: 0.2500 time to fit residues: 70.5684 Evaluate side-chains 208 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063825 restraints weight = 68690.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066737 restraints weight = 24278.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068600 restraints weight = 14336.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069622 restraints weight = 10975.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.070139 restraints weight = 9600.395| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13590 Z= 0.200 Angle : 0.668 8.226 19596 Z= 0.412 Chirality : 0.043 0.362 2232 Planarity : 0.004 0.045 1456 Dihedral : 31.496 172.584 4153 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.77 % Allowed : 17.04 % Favored : 79.19 % 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: 2.11 (0.28), residues: 832 helix: 2.28 (0.21), residues: 580 sheet: -1.96 (1.42), residues: 11 loop : -0.66 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.012 0.001 TYR G 57 PHE 0.012 0.001 PHE A 67 TRP 0.005 0.001 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.20 (13590) covalent geometry : angle 0.66842 / 0.41 (19596) hydrogen bonds : bond 0.04405 / 4.97 ( 818) hydrogen bonds : angle 3.32344 / 4.13 ( 2050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.549 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: B 74 GLU cc_start: 0.8932 (tt0) cc_final: 0.8640 (mt-10) REVERT: C 92 GLU cc_start: 0.8339 (mp0) cc_final: 0.7928 (mp0) REVERT: E 50 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8377 (tt0) REVERT: E 125 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8516 (mm-40) REVERT: G 61 GLU cc_start: 0.8444 (tp30) cc_final: 0.8224 (tp30) REVERT: G 92 GLU cc_start: 0.8873 (mp0) cc_final: 0.8642 (mp0) REVERT: H 68 ASP cc_start: 0.8693 (t0) cc_final: 0.8391 (t0) REVERT: H 93 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: H 113 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8879 (tp30) REVERT: K 409 LYS cc_start: 0.8288 (tttt) cc_final: 0.8034 (pttp) outliers start: 27 outliers final: 25 residues processed: 199 average time/residue: 0.2643 time to fit residues: 72.9073 Evaluate side-chains 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.064105 restraints weight = 68495.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067085 restraints weight = 24634.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068966 restraints weight = 14629.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069919 restraints weight = 11262.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070555 restraints weight = 9944.101| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13590 Z= 0.166 Angle : 0.635 8.398 19596 Z= 0.399 Chirality : 0.042 0.360 2232 Planarity : 0.004 0.052 1456 Dihedral : 31.426 172.305 4153 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.21 % Allowed : 17.32 % Favored : 79.47 % 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: 2.32 (0.29), residues: 832 helix: 2.39 (0.21), residues: 583 sheet: -1.51 (1.46), residues: 11 loop : -0.52 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.011 0.001 TYR G 57 PHE 0.011 0.001 PHE A 67 TRP 0.002 0.001 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (13590) covalent geometry : angle 0.63480 / 0.40 (19596) hydrogen bonds : bond 0.04187 / 4.73 ( 818) hydrogen bonds : angle 3.20132 / 4.00 ( 2050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.481 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: B 74 GLU cc_start: 0.8926 (tt0) cc_final: 0.8633 (mt-10) REVERT: E 50 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8346 (tt0) REVERT: E 125 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8498 (mm-40) REVERT: G 61 GLU cc_start: 0.8471 (tp30) cc_final: 0.8234 (tp30) REVERT: G 92 GLU cc_start: 0.8907 (mp0) cc_final: 0.8678 (mp0) REVERT: H 68 ASP cc_start: 0.8703 (t0) cc_final: 0.8402 (t0) REVERT: H 93 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: H 113 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8837 (tp30) REVERT: K 409 LYS cc_start: 0.8294 (tttt) cc_final: 0.8031 (pttp) outliers start: 23 outliers final: 22 residues processed: 195 average time/residue: 0.2484 time to fit residues: 67.3303 Evaluate side-chains 202 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064903 restraints weight = 68069.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067892 restraints weight = 24350.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069793 restraints weight = 14483.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070816 restraints weight = 11153.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071320 restraints weight = 9798.310| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13590 Z= 0.150 Angle : 0.627 11.297 19596 Z= 0.391 Chirality : 0.041 0.358 2232 Planarity : 0.004 0.050 1456 Dihedral : 31.369 172.528 4153 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.93 % Allowed : 18.02 % Favored : 79.05 % 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: 2.54 (0.29), residues: 832 helix: 2.56 (0.21), residues: 583 sheet: -1.16 (1.52), residues: 11 loop : -0.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.018 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (13590) covalent geometry : angle 0.62713 / 0.39 (19596) hydrogen bonds : bond 0.03997 / 4.50 ( 818) hydrogen bonds : angle 3.07575 / 3.84 ( 2050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8901 (tt0) cc_final: 0.8650 (mt-10) REVERT: D 35 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7102 (mt-10) REVERT: E 125 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8620 (mm-40) REVERT: G 61 GLU cc_start: 0.8437 (tp30) cc_final: 0.8158 (tp30) REVERT: G 92 GLU cc_start: 0.8949 (mp0) cc_final: 0.8700 (mp0) REVERT: H 68 ASP cc_start: 0.8681 (t0) cc_final: 0.8380 (t0) REVERT: H 93 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: H 113 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8869 (tp30) REVERT: K 409 LYS cc_start: 0.8315 (tttt) cc_final: 0.8049 (pttp) outliers start: 21 outliers final: 15 residues processed: 191 average time/residue: 0.2566 time to fit residues: 68.0441 Evaluate side-chains 194 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063624 restraints weight = 68632.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066521 restraints weight = 24604.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068352 restraints weight = 14648.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069317 restraints weight = 11293.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069947 restraints weight = 9968.560| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13590 Z= 0.214 Angle : 0.650 8.196 19596 Z= 0.402 Chirality : 0.041 0.355 2232 Planarity : 0.004 0.054 1456 Dihedral : 31.355 172.507 4153 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.51 % Allowed : 18.72 % Favored : 78.77 % 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: 2.43 (0.29), residues: 832 helix: 2.50 (0.21), residues: 580 sheet: -0.90 (1.59), residues: 11 loop : -0.52 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.012 0.001 TYR G 57 PHE 0.018 0.001 PHE A 78 TRP 0.001 0.001 TRP K 481 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (13590) covalent geometry : angle 0.65002 / 0.40 (19596) hydrogen bonds : bond 0.04289 / 4.84 ( 818) hydrogen bonds : angle 3.22457 / 4.02 ( 2050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.478 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: B 74 GLU cc_start: 0.8906 (tt0) cc_final: 0.8656 (mt-10) REVERT: D 35 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7219 (mt-10) REVERT: E 50 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8290 (tt0) REVERT: E 90 MET cc_start: 0.8403 (mmt) cc_final: 0.8181 (mmp) REVERT: E 125 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8647 (mm-40) REVERT: G 61 GLU cc_start: 0.8466 (tp30) cc_final: 0.8244 (tp30) REVERT: G 92 GLU cc_start: 0.8936 (mp0) cc_final: 0.8701 (mp0) REVERT: H 68 ASP cc_start: 0.8725 (t0) cc_final: 0.8431 (t0) REVERT: K 409 LYS cc_start: 0.8326 (tttt) cc_final: 0.8061 (pttp) outliers start: 18 outliers final: 16 residues processed: 190 average time/residue: 0.2472 time to fit residues: 65.5440 Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063486 restraints weight = 68832.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066381 restraints weight = 24821.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068219 restraints weight = 14834.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069198 restraints weight = 11457.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069733 restraints weight = 10110.964| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13590 Z= 0.206 Angle : 0.655 10.415 19596 Z= 0.403 Chirality : 0.041 0.356 2232 Planarity : 0.004 0.054 1456 Dihedral : 31.327 172.815 4153 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.51 % Allowed : 19.27 % Favored : 78.21 % 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: 2.39 (0.29), residues: 832 helix: 2.48 (0.21), residues: 580 sheet: -0.82 (1.64), residues: 11 loop : -0.57 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.012 0.001 TYR G 57 PHE 0.013 0.001 PHE A 78 TRP 0.001 0.001 TRP K 481 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (13590) covalent geometry : angle 0.65535 / 0.40 (19596) hydrogen bonds : bond 0.04296 / 4.85 ( 818) hydrogen bonds : angle 3.22647 / 4.00 ( 2050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.614 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: B 74 GLU cc_start: 0.8873 (tt0) cc_final: 0.8591 (mt-10) REVERT: C 89 ASN cc_start: 0.8472 (m-40) cc_final: 0.8051 (t0) REVERT: D 35 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7323 (mt-10) REVERT: E 50 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8323 (tt0) REVERT: G 92 GLU cc_start: 0.8931 (mp0) cc_final: 0.8703 (mp0) REVERT: H 68 ASP cc_start: 0.8705 (t0) cc_final: 0.8400 (t0) REVERT: H 93 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: K 409 LYS cc_start: 0.8322 (tttt) cc_final: 0.8050 (pttp) outliers start: 18 outliers final: 16 residues processed: 194 average time/residue: 0.2609 time to fit residues: 70.9416 Evaluate side-chains 196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063870 restraints weight = 68693.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066766 restraints weight = 24708.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068615 restraints weight = 14737.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.069563 restraints weight = 11359.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070174 restraints weight = 10053.441| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.187 Angle : 0.642 8.035 19596 Z= 0.397 Chirality : 0.041 0.355 2232 Planarity : 0.004 0.054 1456 Dihedral : 31.282 172.871 4153 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.23 % Allowed : 19.69 % Favored : 78.07 % 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: 2.43 (0.29), residues: 832 helix: 2.51 (0.21), residues: 580 sheet: -0.72 (1.67), residues: 11 loop : -0.57 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.011 0.001 TYR H 40 PHE 0.012 0.001 PHE A 78 TRP 0.001 0.001 TRP K 481 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 (13590) covalent geometry : angle 0.64243 / 0.40 (19596) hydrogen bonds : bond 0.04219 / 4.75 ( 818) hydrogen bonds : angle 3.17060 / 3.97 ( 2050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.65 seconds wall clock time: 67 minutes 37.15 seconds (4057.15 seconds total)