Starting phenix.real_space_refine on Wed Aug 5 23:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2026/8v25_42898.map" } resolution = 3.32 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= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 16 5.16 5 C 7063 2.51 5 N 2387 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12689 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG K 74 " occ=0.95 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.95 residue: pdb=" N GLY K 75 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.65 Time building chain proxies: 2.91, per 1000 atoms: 0.23 Number of scatterers: 12689 At special positions: 0 Unit cell: (101.85, 122.22, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 288 15.00 O 2935 8.00 N 2387 7.00 C 7063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 366.8 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 66.9% alpha, 4.2% beta 138 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.520A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.803A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.622A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.099A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.656A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.649A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.588A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.558A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.599A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.607A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.533A 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 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.190A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.543A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.506A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.520A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.611A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.109A 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: 7.324A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.895A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.346A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2639 1.33 - 1.45: 4191 1.45 - 1.57: 6065 1.57 - 1.69: 576 1.69 - 1.81: 27 Bond restraints: 13498 Sorted by residual: bond pdb=" C1' DT I -72 " pdb=" N1 DT I -72 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.31e+01 bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.468 1.389 0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C1' DC J 70 " pdb=" N1 DC J 70 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.468 1.391 0.077 1.40e-02 5.10e+03 3.04e+01 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 18881 2.17 - 4.33: 549 4.33 - 6.50: 32 6.50 - 8.66: 3 8.66 - 10.83: 1 Bond angle restraints: 19466 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 119.70 108.87 10.83 1.20e+00 6.94e-01 8.15e+01 angle pdb=" C3' DG I 71 " pdb=" O3' DG I 71 " pdb=" P DA I 72 " ideal model delta sigma weight residual 119.70 112.34 7.36 1.20e+00 6.94e-01 3.76e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 119.70 113.10 6.60 1.20e+00 6.94e-01 3.02e+01 angle pdb=" O4' DA I -67 " pdb=" C4' DA I -67 " pdb=" C3' DA I -67 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 119.70 114.19 5.51 1.20e+00 6.94e-01 2.11e+01 ... (remaining 19461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6017 35.81 - 71.62: 1378 71.62 - 107.44: 8 107.44 - 143.25: 4 143.25 - 179.06: 1 Dihedral angle restraints: 7408 sinusoidal: 4945 harmonic: 2463 Sorted by residual: dihedral pdb=" CA MET K 1 " pdb=" C MET K 1 " pdb=" N GLN K 2 " pdb=" CA GLN K 2 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 39.06 -179.06 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 94.61 125.39 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 7405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2148 0.100 - 0.200: 65 0.200 - 0.300: 0 0.300 - 0.400: 0 0.400 - 0.500: 6 Chirality restraints: 2219 Sorted by residual: chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" P DG I 71 " pdb=" OP1 DG I 71 " pdb=" OP2 DG I 71 " pdb=" O5' DG I 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 2216 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.03e-02 3.15e+00 pdb=" N9 DG I 47 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 38 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.022 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2675 2.81 - 3.33: 10636 3.33 - 3.85: 22521 3.85 - 4.38: 26626 4.38 - 4.90: 38325 Nonbonded interactions: 100783 Sorted by model distance: nonbonded pdb=" OE1 GLU K 51 " pdb=" OH TYR K 59 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.303 3.040 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.313 3.120 nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.315 3.040 ... (remaining 100778 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 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.006 0.081 13498 Z= 0.527 Angle : 0.755 10.831 19466 Z= 0.656 Chirality : 0.050 0.500 2219 Planarity : 0.004 0.038 1463 Dihedral : 27.354 179.059 5816 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.42 % Allowed : 20.34 % Favored : 79.24 % 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: 2.59 (0.30), residues: 831 helix: 3.13 (0.22), residues: 523 sheet: 1.31 (0.88), residues: 26 loop : -1.14 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.53 (13498) covalent geometry : angle 0.75534 / 0.66 (19466) hydrogen bonds : bond 0.12257 / 8.59 ( 775) hydrogen bonds : angle 3.86195 / 2.62 ( 1953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.354 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.1683 time to fit residues: 29.2241 Evaluate side-chains 129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain F residue 85 ASP 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: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0020 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062337 restraints weight = 28875.866| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.97 r_work: 0.2657 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13498 Z= 0.162 Angle : 0.603 7.753 19466 Z= 0.366 Chirality : 0.044 0.230 2219 Planarity : 0.004 0.044 1463 Dihedral : 29.727 177.123 4118 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 19.64 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.30), residues: 831 helix: 3.07 (0.22), residues: 547 sheet: 1.57 (0.90), residues: 26 loop : -1.14 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (13498) covalent geometry : angle 0.60297 / 0.37 (19466) hydrogen bonds : bond 0.06611 / 4.44 ( 775) hydrogen bonds : angle 3.12320 / 2.20 ( 1953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.334 Fit side-chains REVERT: B 24 ASP cc_start: 0.7860 (t0) cc_final: 0.7649 (t0) REVERT: B 27 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: F 24 ASP cc_start: 0.7525 (p0) cc_final: 0.7267 (p0) REVERT: H 65 ASP cc_start: 0.9120 (t0) cc_final: 0.8903 (t0) REVERT: K 1 MET cc_start: 0.7178 (ppp) cc_final: 0.6963 (ppp) outliers start: 14 outliers final: 12 residues processed: 136 average time/residue: 0.1496 time to fit residues: 26.6426 Evaluate side-chains 138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 99 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062881 restraints weight = 28870.637| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.97 r_work: 0.2667 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13498 Z= 0.151 Angle : 0.568 7.769 19466 Z= 0.348 Chirality : 0.042 0.227 2219 Planarity : 0.004 0.052 1463 Dihedral : 29.754 177.200 4114 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 18.65 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.30), residues: 831 helix: 3.20 (0.22), residues: 550 sheet: 1.32 (0.85), residues: 26 loop : -1.18 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (13498) covalent geometry : angle 0.56847 / 0.35 (19466) hydrogen bonds : bond 0.06094 / 4.08 ( 775) hydrogen bonds : angle 2.95846 / 2.07 ( 1953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7996 (t0) cc_final: 0.7688 (t0) REVERT: B 25 ASN cc_start: 0.8855 (m-40) cc_final: 0.8392 (m110) REVERT: B 27 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8575 (mp10) REVERT: F 24 ASP cc_start: 0.7641 (p0) cc_final: 0.7393 (p0) REVERT: F 92 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8447 (mtp85) REVERT: K 1 MET cc_start: 0.7090 (ppp) cc_final: 0.6494 (ppp) outliers start: 18 outliers final: 9 residues processed: 144 average time/residue: 0.1453 time to fit residues: 27.5670 Evaluate side-chains 138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 26 optimal weight: 0.0170 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.065292 restraints weight = 28790.237| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.89 r_work: 0.2730 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13498 Z= 0.138 Angle : 0.547 8.159 19466 Z= 0.337 Chirality : 0.041 0.225 2219 Planarity : 0.004 0.059 1463 Dihedral : 29.734 176.374 4114 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.95 % Allowed : 19.64 % Favored : 77.42 % 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: 3.00 (0.30), residues: 831 helix: 3.31 (0.22), residues: 553 sheet: 1.29 (0.86), residues: 26 loop : -1.18 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.009 0.001 TYR K 59 PHE 0.007 0.001 PHE K 4 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.14 (13498) covalent geometry : angle 0.54682 / 0.34 (19466) hydrogen bonds : bond 0.05073 / 3.38 ( 775) hydrogen bonds : angle 2.76437 / 1.91 ( 1953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8917 (tt0) cc_final: 0.8277 (tt0) REVERT: B 24 ASP cc_start: 0.7935 (t0) cc_final: 0.7590 (t0) REVERT: B 25 ASN cc_start: 0.8782 (m-40) cc_final: 0.8216 (m110) REVERT: B 27 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: F 92 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8408 (mtp85) REVERT: H 65 ASP cc_start: 0.9110 (t0) cc_final: 0.8788 (t0) REVERT: K 1 MET cc_start: 0.7382 (ppp) cc_final: 0.6829 (ppp) outliers start: 21 outliers final: 13 residues processed: 149 average time/residue: 0.1275 time to fit residues: 25.2035 Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.064425 restraints weight = 28877.646| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.98 r_work: 0.2711 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13498 Z= 0.142 Angle : 0.547 7.667 19466 Z= 0.334 Chirality : 0.041 0.220 2219 Planarity : 0.004 0.055 1463 Dihedral : 29.768 176.490 4114 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.66 % Allowed : 20.34 % Favored : 77.00 % 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: 3.01 (0.30), residues: 831 helix: 3.34 (0.22), residues: 553 sheet: 0.92 (0.84), residues: 26 loop : -1.18 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.006 0.001 TYR H 37 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (13498) covalent geometry : angle 0.54722 / 0.33 (19466) hydrogen bonds : bond 0.05321 / 3.55 ( 775) hydrogen bonds : angle 2.78147 / 1.93 ( 1953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8921 (tt0) cc_final: 0.8242 (tt0) REVERT: B 24 ASP cc_start: 0.7956 (t0) cc_final: 0.7608 (t0) REVERT: B 25 ASN cc_start: 0.8833 (m-40) cc_final: 0.8235 (m110) REVERT: B 27 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: F 24 ASP cc_start: 0.7839 (p0) cc_final: 0.7572 (p0) REVERT: F 92 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8445 (mtp85) REVERT: H 65 ASP cc_start: 0.9124 (t0) cc_final: 0.8791 (t0) REVERT: K 1 MET cc_start: 0.7213 (ppp) cc_final: 0.6428 (ppp) outliers start: 19 outliers final: 13 residues processed: 143 average time/residue: 0.1344 time to fit residues: 25.6754 Evaluate side-chains 144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064640 restraints weight = 28743.992| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.89 r_work: 0.2717 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13498 Z= 0.140 Angle : 0.545 7.682 19466 Z= 0.332 Chirality : 0.041 0.219 2219 Planarity : 0.004 0.055 1463 Dihedral : 29.785 176.254 4114 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.52 % Allowed : 20.62 % Favored : 76.86 % 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: 3.04 (0.30), residues: 831 helix: 3.36 (0.22), residues: 554 sheet: 0.79 (0.83), residues: 26 loop : -1.15 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.006 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (13498) covalent geometry : angle 0.54523 / 0.33 (19466) hydrogen bonds : bond 0.05328 / 3.55 ( 775) hydrogen bonds : angle 2.75139 / 1.91 ( 1953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8905 (tt0) cc_final: 0.8180 (tt0) REVERT: B 24 ASP cc_start: 0.7954 (t0) cc_final: 0.7613 (t0) REVERT: B 25 ASN cc_start: 0.8827 (m-40) cc_final: 0.8187 (m110) REVERT: B 27 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: F 92 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8411 (mtp85) REVERT: G 42 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: H 65 ASP cc_start: 0.9114 (t0) cc_final: 0.8762 (t0) REVERT: K 1 MET cc_start: 0.7025 (ppp) cc_final: 0.6206 (ppp) outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.1363 time to fit residues: 25.9746 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.094277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.064416 restraints weight = 28730.263| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.89 r_work: 0.2713 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13498 Z= 0.142 Angle : 0.550 7.714 19466 Z= 0.333 Chirality : 0.041 0.217 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.793 176.295 4114 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.52 % Allowed : 20.62 % Favored : 76.86 % 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: 3.05 (0.30), residues: 831 helix: 3.37 (0.22), residues: 555 sheet: 0.50 (0.81), residues: 26 loop : -1.16 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.010 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (13498) covalent geometry : angle 0.55049 / 0.33 (19466) hydrogen bonds : bond 0.05427 / 3.61 ( 775) hydrogen bonds : angle 2.75356 / 1.91 ( 1953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8903 (tt0) cc_final: 0.8147 (tt0) REVERT: B 24 ASP cc_start: 0.7953 (t0) cc_final: 0.7626 (t0) REVERT: B 25 ASN cc_start: 0.8841 (m-40) cc_final: 0.8175 (m110) REVERT: B 27 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8548 (mp10) REVERT: F 24 ASP cc_start: 0.7943 (p0) cc_final: 0.7654 (p0) REVERT: F 92 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8392 (mtp85) REVERT: G 42 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7973 (mtm180) REVERT: H 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8768 (t0) REVERT: K 1 MET cc_start: 0.7128 (ppp) cc_final: 0.6197 (ppp) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.1524 time to fit residues: 28.4844 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.064414 restraints weight = 28549.814| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.87 r_work: 0.2714 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13498 Z= 0.142 Angle : 0.549 7.749 19466 Z= 0.332 Chirality : 0.041 0.217 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.801 176.217 4114 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 21.32 % Favored : 76.16 % 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: 3.04 (0.30), residues: 831 helix: 3.38 (0.22), residues: 555 sheet: 0.40 (0.81), residues: 26 loop : -1.19 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (13498) covalent geometry : angle 0.54937 / 0.33 (19466) hydrogen bonds : bond 0.05458 / 3.63 ( 775) hydrogen bonds : angle 2.73776 / 1.91 ( 1953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: B 24 ASP cc_start: 0.7997 (t0) cc_final: 0.7755 (t0) REVERT: B 27 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: F 92 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8391 (mtp85) REVERT: G 42 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7975 (mtm180) REVERT: H 65 ASP cc_start: 0.9134 (t0) cc_final: 0.8765 (t0) REVERT: K 1 MET cc_start: 0.7217 (ppp) cc_final: 0.6322 (ppp) outliers start: 18 outliers final: 13 residues processed: 145 average time/residue: 0.1488 time to fit residues: 28.3088 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.063226 restraints weight = 28659.568| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.88 r_work: 0.2685 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13498 Z= 0.159 Angle : 0.573 7.863 19466 Z= 0.342 Chirality : 0.042 0.216 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.825 176.370 4114 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 21.04 % Favored : 76.02 % 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: 2.96 (0.30), residues: 831 helix: 3.32 (0.22), residues: 555 sheet: 0.22 (0.96), residues: 20 loop : -1.17 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.009 0.001 TYR K 59 PHE 0.008 0.001 PHE H 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (13498) covalent geometry : angle 0.57308 / 0.34 (19466) hydrogen bonds : bond 0.05927 / 3.95 ( 775) hydrogen bonds : angle 2.83639 / 1.98 ( 1953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.399 Fit side-chains REVERT: A 59 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: B 24 ASP cc_start: 0.8018 (t0) cc_final: 0.7816 (t0) REVERT: B 27 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: F 92 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8395 (mtp85) REVERT: G 42 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7972 (mtm180) REVERT: H 65 ASP cc_start: 0.9130 (t0) cc_final: 0.8756 (t0) REVERT: K 1 MET cc_start: 0.7366 (ppp) cc_final: 0.6424 (ppp) outliers start: 21 outliers final: 14 residues processed: 142 average time/residue: 0.1507 time to fit residues: 28.0402 Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.063290 restraints weight = 28846.020| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.89 r_work: 0.2686 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 13498 Z= 0.203 Angle : 0.786 59.197 19466 Z= 0.475 Chirality : 0.042 0.373 2219 Planarity : 0.004 0.055 1463 Dihedral : 29.828 176.377 4114 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 21.46 % Favored : 75.74 % 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: 2.97 (0.30), residues: 831 helix: 3.32 (0.22), residues: 555 sheet: 0.23 (0.97), residues: 20 loop : -1.17 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (13498) covalent geometry : angle 0.78571 / 0.48 (19466) hydrogen bonds : bond 0.05881 / 3.91 ( 775) hydrogen bonds : angle 2.83391 / 1.98 ( 1953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.238 Fit side-chains REVERT: A 59 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: B 24 ASP cc_start: 0.8021 (t0) cc_final: 0.7804 (t0) REVERT: B 27 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: F 92 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: G 42 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7966 (mtm180) REVERT: H 65 ASP cc_start: 0.9148 (t0) cc_final: 0.8776 (t0) REVERT: K 1 MET cc_start: 0.7369 (ppp) cc_final: 0.6437 (ppp) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.1577 time to fit residues: 28.5150 Evaluate side-chains 144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 9 optimal weight: 0.3980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.063208 restraints weight = 28746.904| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.96 r_work: 0.2677 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 13498 Z= 0.203 Angle : 0.786 59.197 19466 Z= 0.475 Chirality : 0.042 0.373 2219 Planarity : 0.004 0.055 1463 Dihedral : 29.828 176.377 4114 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.52 % Allowed : 21.74 % Favored : 75.74 % 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: 2.97 (0.30), residues: 831 helix: 3.32 (0.22), residues: 555 sheet: 0.23 (0.97), residues: 20 loop : -1.17 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (13498) covalent geometry : angle 0.78572 / 0.48 (19466) hydrogen bonds : bond 0.05881 / 3.91 ( 775) hydrogen bonds : angle 2.83391 / 1.98 ( 1953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.81 seconds wall clock time: 37 minutes 24.72 seconds (2244.72 seconds total)