Starting phenix.real_space_refine on Sun Sep 13 10:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scz_25043/09_2026/7scz_25043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scz_25043/09_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_25043/09_2026/7scz_25043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scz_25043/09_2026/7scz_25043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scz_25043/09_2026/7scz_25043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scz_25043/09_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-2.2.1-6174/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: 3.86, per 1000 atoms: 0.17 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: 2.18 Conformation dependent library (CDL) restraints added in 464.5 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: 3.54 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: 4.57 Time building geometry restraints manager: 3.01 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: 43094 6.26 - 12.51: 485 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: 1.040 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: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- 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= 1.341 Angle : 1.927 13.497 19596 Z= 1.947 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 1.92666 / 1.95 (19596) hydrogen bonds : bond 0.13010 / 14.51 ( 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 : 0.493 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: A 108 ASN cc_start: 0.8343 (t0) cc_final: 0.8025 (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: 0.7280 (p) REVERT: C 90 ASP cc_start: 0.6953 (t70) cc_final: 0.6673 (t70) REVERT: D 59 MET cc_start: 0.8395 (tpp) cc_final: 0.8193 (tpp) REVERT: D 89 ILE cc_start: 0.9266 (mt) cc_final: 0.8897 (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: 0.8057 (tp30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3061 time to fit residues: 122.2395 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.094677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065895 restraints weight = 67637.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069067 restraints weight = 24184.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071089 restraints weight = 14198.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072195 restraints weight = 10842.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072817 restraints weight = 9461.657| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13590 Z= 0.205 Angle : 0.875 8.080 19596 Z= 0.524 Chirality : 0.054 0.418 2232 Planarity : 0.007 0.070 1456 Dihedral : 31.643 177.458 4153 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.79 % Allowed : 11.59 % 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: 1.28 (0.27), residues: 832 helix: 1.43 (0.21), residues: 582 sheet: -1.67 (1.48), residues: 11 loop : -0.34 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.017 0.002 TYR C 57 PHE 0.027 0.002 PHE A 67 TRP 0.005 0.002 TRP K 481 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.21 (13590) covalent geometry : angle 0.87528 / 0.52 (19596) hydrogen bonds : bond 0.06729 / 7.67 ( 818) hydrogen bonds : angle 3.86782 / 4.83 ( 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 233 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7776 (tp30) cc_final: 0.7455 (tp30) REVERT: A 90 MET cc_start: 0.8178 (mmm) cc_final: 0.7942 (mmm) REVERT: B 77 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8931 (mtpp) REVERT: E 50 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8139 (tt0) REVERT: E 94 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7997 (tp30) REVERT: G 61 GLU cc_start: 0.8617 (tp30) cc_final: 0.8404 (tp30) REVERT: H 62 MET cc_start: 0.9145 (mmp) cc_final: 0.8709 (mmt) REVERT: H 68 ASP cc_start: 0.8405 (t0) cc_final: 0.8101 (t0) REVERT: K 409 LYS cc_start: 0.8251 (tttt) cc_final: 0.8004 (pttp) outliers start: 20 outliers final: 16 residues processed: 223 average time/residue: 0.2505 time to fit residues: 77.3282 Evaluate side-chains 214 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 47 SER 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 87 SER 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 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: 1.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.091422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063792 restraints weight = 68333.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.066735 restraints weight = 24172.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.068593 restraints weight = 14206.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069683 restraints weight = 10820.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070224 restraints weight = 9395.886| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13590 Z= 0.239 Angle : 0.767 8.862 19596 Z= 0.471 Chirality : 0.048 0.376 2232 Planarity : 0.005 0.047 1456 Dihedral : 31.628 171.640 4153 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.49 % Allowed : 13.27 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.28), residues: 832 helix: 1.84 (0.21), residues: 582 sheet: -1.72 (1.53), residues: 11 loop : -0.63 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.015 0.002 TYR F 98 PHE 0.023 0.002 PHE A 67 TRP 0.003 0.001 TRP K 481 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.24 (13590) covalent geometry : angle 0.76737 / 0.47 (19596) hydrogen bonds : bond 0.05611 / 6.35 ( 818) hydrogen bonds : angle 3.65638 / 4.59 ( 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 223 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7901 (tp30) cc_final: 0.7687 (tp30) REVERT: E 50 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8315 (tt0) REVERT: E 73 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 94 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7831 (tp30) REVERT: E 125 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8423 (mm-40) REVERT: F 25 ASN cc_start: 0.8546 (m110) cc_final: 0.8253 (m110) REVERT: F 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8534 (m-30) REVERT: G 92 GLU cc_start: 0.8811 (mp0) cc_final: 0.8542 (mp0) REVERT: K 409 LYS cc_start: 0.8232 (tttt) cc_final: 0.7981 (pttp) outliers start: 25 outliers final: 22 residues processed: 214 average time/residue: 0.2491 time to fit residues: 74.4208 Evaluate side-chains 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 C residue 99 ARG Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 87 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 62 ILE Chi-restraints excluded: chain H residue 36 SER 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: 3.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.091874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064254 restraints weight = 68391.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067162 restraints weight = 24169.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069073 restraints weight = 14249.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.070144 restraints weight = 10818.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070705 restraints weight = 9416.647| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13590 Z= 0.189 Angle : 0.696 8.233 19596 Z= 0.430 Chirality : 0.045 0.368 2232 Planarity : 0.004 0.055 1456 Dihedral : 31.583 172.989 4153 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.63 % Allowed : 14.94 % Favored : 81.42 % 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: 1.92 (0.28), residues: 832 helix: 2.09 (0.21), residues: 582 sheet: -1.72 (1.51), residues: 11 loop : -0.63 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 452 TYR 0.027 0.002 TYR D 40 PHE 0.013 0.001 PHE K 458 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 0.00331 / 0.19 (13590) covalent geometry : angle 0.69559 / 0.43 (19596) hydrogen bonds : bond 0.04724 / 5.36 ( 818) hydrogen bonds : angle 3.45220 / 4.32 ( 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 215 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 74 GLU cc_start: 0.8856 (tt0) cc_final: 0.8408 (mt-10) REVERT: D 35 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7069 (mt-10) REVERT: E 50 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8316 (tt0) REVERT: E 73 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8018 (tm-30) REVERT: E 94 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7750 (tp30) REVERT: E 125 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8367 (mm-40) REVERT: F 25 ASN cc_start: 0.8545 (m110) cc_final: 0.8263 (m110) REVERT: G 92 GLU cc_start: 0.8840 (mp0) cc_final: 0.8496 (mp0) REVERT: G 104 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8738 (mm110) REVERT: H 68 ASP cc_start: 0.8585 (t0) cc_final: 0.8294 (t0) REVERT: K 409 LYS cc_start: 0.8227 (tttt) cc_final: 0.7990 (pttp) outliers start: 26 outliers final: 24 residues processed: 203 average time/residue: 0.2497 time to fit residues: 71.5805 Evaluate side-chains 211 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 87 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 96 optimal weight: 0.0870 chunk 20 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.5362 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.092287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064388 restraints weight = 67985.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067354 restraints weight = 24316.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069273 restraints weight = 14372.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070313 restraints weight = 10948.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070889 restraints weight = 9562.147| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13590 Z= 0.175 Angle : 0.671 10.596 19596 Z= 0.418 Chirality : 0.043 0.365 2232 Planarity : 0.004 0.047 1456 Dihedral : 31.492 171.569 4153 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.21 % Allowed : 16.06 % Favored : 80.73 % 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: 2.24 (0.28), residues: 832 helix: 2.34 (0.21), residues: 583 sheet: -1.93 (1.45), residues: 11 loop : -0.53 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 92 TYR 0.026 0.002 TYR D 40 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 0.00303 / 0.17 (13590) covalent geometry : angle 0.67098 / 0.42 (19596) hydrogen bonds : bond 0.04337 / 4.90 ( 818) hydrogen bonds : angle 3.27512 / 4.08 ( 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 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8871 (tt0) cc_final: 0.8411 (mt-10) REVERT: C 92 GLU cc_start: 0.8096 (mp0) cc_final: 0.7682 (mp0) REVERT: D 35 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7077 (mt-10) REVERT: D 42 TYR cc_start: 0.7804 (t80) cc_final: 0.7415 (t80) REVERT: E 94 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8012 (tp30) REVERT: E 125 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8425 (mm-40) REVERT: F 25 ASN cc_start: 0.8437 (m110) cc_final: 0.8217 (m110) REVERT: G 61 GLU cc_start: 0.8502 (tp30) cc_final: 0.8256 (tp30) REVERT: G 92 GLU cc_start: 0.8858 (mp0) cc_final: 0.8510 (mp0) REVERT: G 104 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8684 (mm110) REVERT: H 68 ASP cc_start: 0.8663 (t0) cc_final: 0.8363 (t0) REVERT: H 93 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: K 409 LYS cc_start: 0.8281 (tttt) cc_final: 0.8037 (pttp) outliers start: 23 outliers final: 20 residues processed: 198 average time/residue: 0.2355 time to fit residues: 65.3651 Evaluate side-chains 204 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 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 D residue 87 SER 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 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.091240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.063230 restraints weight = 69032.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066165 restraints weight = 24884.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068019 restraints weight = 14708.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069006 restraints weight = 11286.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069578 restraints weight = 9907.753| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13590 Z= 0.229 Angle : 0.686 8.761 19596 Z= 0.420 Chirality : 0.043 0.358 2232 Planarity : 0.004 0.047 1456 Dihedral : 31.438 172.306 4153 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.49 % Allowed : 17.04 % 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: 2.12 (0.28), residues: 832 helix: 2.30 (0.21), residues: 580 sheet: -1.81 (1.42), residues: 11 loop : -0.70 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.016 0.002 TYR D 40 PHE 0.010 0.001 PHE A 67 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (13590) covalent geometry : angle 0.68570 / 0.42 (19596) hydrogen bonds : bond 0.04576 / 5.21 ( 818) hydrogen bonds : angle 3.40322 / 4.25 ( 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 207 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.506 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: 0.8933 (tt0) cc_final: 0.8643 (mt-10) REVERT: D 35 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7190 (mt-10) REVERT: D 42 TYR cc_start: 0.7911 (t80) cc_final: 0.7542 (t80) REVERT: E 50 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8381 (tt0) REVERT: E 125 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8460 (mm-40) REVERT: G 61 GLU cc_start: 0.8480 (tp30) cc_final: 0.8255 (tp30) REVERT: G 92 GLU cc_start: 0.8882 (mp0) cc_final: 0.8676 (mp0) REVERT: G 104 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8459 (mm110) REVERT: H 93 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: K 409 LYS cc_start: 0.8292 (tttt) cc_final: 0.8037 (pttp) outliers start: 25 outliers final: 23 residues processed: 196 average time/residue: 0.2556 time to fit residues: 70.7240 Evaluate side-chains 202 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 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 D residue 87 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE 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 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: 3.9990 chunk 30 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.092170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.064039 restraints weight = 68667.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067002 restraints weight = 24661.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068880 restraints weight = 14618.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069890 restraints weight = 11235.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.070389 restraints weight = 9860.494| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13590 Z= 0.171 Angle : 0.653 9.146 19596 Z= 0.404 Chirality : 0.042 0.355 2232 Planarity : 0.004 0.053 1456 Dihedral : 31.375 172.138 4153 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.93 % Allowed : 17.74 % Favored : 79.33 % 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: 2.41 (0.21), residues: 583 sheet: -1.52 (1.48), residues: 11 loop : -0.57 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.020 0.002 TYR D 40 PHE 0.010 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 0.00300 / 0.17 (13590) covalent geometry : angle 0.65252 / 0.40 (19596) hydrogen bonds : bond 0.04204 / 4.76 ( 818) hydrogen bonds : angle 3.20900 / 3.99 ( 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 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.419 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: 0.8902 (tt0) cc_final: 0.8595 (mt-10) REVERT: D 42 TYR cc_start: 0.7874 (t80) cc_final: 0.7532 (t80) REVERT: E 50 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8342 (tt0) REVERT: E 125 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8470 (mm-40) REVERT: G 61 GLU cc_start: 0.8463 (tp30) cc_final: 0.8224 (tp30) REVERT: H 68 ASP cc_start: 0.8672 (t0) cc_final: 0.8399 (t0) REVERT: H 93 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: H 113 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8835 (tp30) REVERT: K 409 LYS cc_start: 0.8294 (tttt) cc_final: 0.8029 (pttp) outliers start: 21 outliers final: 19 residues processed: 191 average time/residue: 0.2405 time to fit residues: 64.1758 Evaluate side-chains 199 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 30 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 D residue 87 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 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 9.9990 chunk 37 optimal weight: 0.0010 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.092280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064488 restraints weight = 68148.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067428 restraints weight = 24025.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069235 restraints weight = 14159.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070311 restraints weight = 10914.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070865 restraints weight = 9529.379| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13590 Z= 0.167 Angle : 0.643 8.611 19596 Z= 0.398 Chirality : 0.041 0.355 2232 Planarity : 0.004 0.050 1456 Dihedral : 31.308 172.321 4153 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.21 % Allowed : 17.46 % Favored : 79.33 % 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: 2.44 (0.29), residues: 832 helix: 2.49 (0.21), residues: 583 sheet: -1.16 (1.55), residues: 11 loop : -0.52 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.015 0.001 TYR D 40 PHE 0.009 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 0.00294 / 0.17 (13590) covalent geometry : angle 0.64335 / 0.40 (19596) hydrogen bonds : bond 0.04121 / 4.67 ( 818) hydrogen bonds : angle 3.15434 / 3.96 ( 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 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.473 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: 0.8900 (tt0) cc_final: 0.8650 (mt-10) REVERT: D 35 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7084 (mt-10) REVERT: D 42 TYR cc_start: 0.7916 (t80) cc_final: 0.7553 (t80) REVERT: D 87 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.7866 (p) REVERT: E 125 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8637 (mm-40) REVERT: G 61 GLU cc_start: 0.8415 (tp30) cc_final: 0.8137 (tp30) REVERT: G 91 GLU cc_start: 0.8224 (tp30) cc_final: 0.7992 (tp30) REVERT: H 68 ASP cc_start: 0.8680 (t0) cc_final: 0.8421 (t0) REVERT: H 93 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: H 113 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8854 (tp30) REVERT: K 409 LYS cc_start: 0.8319 (tttt) cc_final: 0.8049 (pttp) outliers start: 23 outliers final: 18 residues processed: 193 average time/residue: 0.2373 time to fit residues: 64.7557 Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 87 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 G residue 16 THR Chi-restraints excluded: chain G residue 59 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 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064911 restraints weight = 68356.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067829 restraints weight = 23833.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069692 restraints weight = 14035.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070670 restraints weight = 10729.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071297 restraints weight = 9442.283| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13590 Z= 0.155 Angle : 0.638 9.620 19596 Z= 0.396 Chirality : 0.041 0.356 2232 Planarity : 0.004 0.053 1456 Dihedral : 31.248 172.397 4153 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.37 % Allowed : 18.16 % 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: 2.56 (0.29), residues: 832 helix: 2.58 (0.21), residues: 583 sheet: -0.91 (1.60), residues: 11 loop : -0.48 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.018 0.001 TYR D 40 PHE 0.010 0.001 PHE K 458 TRP 0.002 0.001 TRP K 481 HIS 0.004 0.001 HIS K 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (13590) covalent geometry : angle 0.63837 / 0.40 (19596) hydrogen bonds : bond 0.03988 / 4.50 ( 818) hydrogen bonds : angle 3.06997 / 3.84 ( 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 200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.8666 (m-80) cc_final: 0.8463 (m-10) REVERT: B 74 GLU cc_start: 0.8897 (tt0) cc_final: 0.8644 (mt-10) REVERT: C 92 GLU cc_start: 0.8055 (mp0) cc_final: 0.7840 (mp0) REVERT: D 35 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 42 TYR cc_start: 0.7897 (t80) cc_final: 0.7533 (t80) REVERT: D 87 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.7780 (p) REVERT: E 50 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8245 (tt0) REVERT: E 125 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8646 (mm-40) REVERT: G 61 GLU cc_start: 0.8420 (tp30) cc_final: 0.8137 (tp30) REVERT: G 110 ASN cc_start: 0.8791 (t0) cc_final: 0.8197 (p0) REVERT: H 68 ASP cc_start: 0.8678 (t0) cc_final: 0.8426 (t0) REVERT: H 93 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: H 113 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8846 (tp30) REVERT: K 409 LYS cc_start: 0.8306 (tttt) cc_final: 0.8034 (pttp) outliers start: 17 outliers final: 15 residues processed: 194 average time/residue: 0.2659 time to fit residues: 72.2415 Evaluate side-chains 199 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 87 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU 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 85 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.090487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062503 restraints weight = 69315.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065351 restraints weight = 25191.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067179 restraints weight = 15073.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068112 restraints weight = 11591.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068763 restraints weight = 10239.980| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13590 Z= 0.276 Angle : 0.703 8.625 19596 Z= 0.423 Chirality : 0.043 0.355 2232 Planarity : 0.004 0.054 1456 Dihedral : 31.241 172.474 4153 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.65 % Allowed : 18.44 % Favored : 78.91 % 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: 2.21 (0.28), residues: 832 helix: 2.37 (0.21), residues: 580 sheet: -0.88 (1.64), residues: 11 loop : -0.73 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.017 0.002 TYR D 40 PHE 0.014 0.002 PHE C 25 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.28 (13590) covalent geometry : angle 0.70250 / 0.42 (19596) hydrogen bonds : bond 0.04746 / 5.39 ( 818) hydrogen bonds : angle 3.42004 / 4.27 ( 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 200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.506 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: 0.8914 (tt0) cc_final: 0.8640 (mt-10) REVERT: D 35 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7270 (mt-10) REVERT: D 42 TYR cc_start: 0.7964 (t80) cc_final: 0.7672 (t80) REVERT: D 87 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.7909 (p) REVERT: E 50 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8430 (tt0) REVERT: G 84 GLN cc_start: 0.8656 (tp40) cc_final: 0.8394 (tp-100) REVERT: H 93 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: K 409 LYS cc_start: 0.8326 (tttt) cc_final: 0.8048 (pttp) outliers start: 19 outliers final: 17 residues processed: 193 average time/residue: 0.2485 time to fit residues: 67.0301 Evaluate side-chains 196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 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 D residue 87 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 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 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 102 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063736 restraints weight = 68844.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.066613 restraints weight = 24711.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068483 restraints weight = 14762.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.069477 restraints weight = 11358.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069946 restraints weight = 9989.100| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13590 Z= 0.180 Angle : 0.662 8.500 19596 Z= 0.404 Chirality : 0.041 0.355 2232 Planarity : 0.004 0.054 1456 Dihedral : 31.220 172.937 4153 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 19.13 % Favored : 78.35 % 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: 2.38 (0.29), residues: 832 helix: 2.46 (0.21), residues: 583 sheet: -0.76 (1.67), residues: 11 loop : -0.60 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.019 0.002 TYR D 40 PHE 0.011 0.001 PHE C 25 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 0.00333 / 0.18 (13590) covalent geometry : angle 0.66196 / 0.40 (19596) hydrogen bonds : bond 0.04252 / 4.81 ( 818) hydrogen bonds : angle 3.21410 / 4.02 ( 2050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.98 seconds wall clock time: 66 minutes 17.88 seconds (3977.88 seconds total)