Starting phenix.real_space_refine on Fri Jul 3 06:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kq2_62494/07_2026/9kq2_62494.map" } resolution = 3.9 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= 0.023 sd= 0.527 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 Zn 2 6.06 5 P 288 5.49 5 S 23 5.16 5 C 6955 2.51 5 N 2349 2.21 5 O 2897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12514 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, '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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 777 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11993 SG CYS K 31 72.905 49.898 81.288 1.00186.06 S ATOM 12143 SG CYS K 51 74.420 46.621 80.056 1.00181.69 S ATOM 12167 SG CYS K 54 71.816 46.577 82.781 1.00184.22 S ATOM 11884 SG CYS K 16 85.402 49.184 74.664 1.00245.85 S ATOM 11902 SG CYS K 19 86.439 47.014 72.389 1.00255.12 S ATOM 12032 SG CYS K 36 85.010 50.023 72.401 1.00225.54 S ATOM 12054 SG CYS K 39 82.711 48.783 71.742 1.00 30.00 S Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12514 At special positions: 0 Unit cell: (110.21, 116.63, 121.98, 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) Zn 2 29.99 S 23 16.00 P 288 15.00 O 2897 8.00 N 2349 7.00 C 6955 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: 0.96 Conformation dependent library (CDL) restraints added in 406.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 31 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 16 " Number of angles added : 6 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 72.3% alpha, 2.4% beta 133 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.819A 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 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.502A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.053A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.453A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.732A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.541A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.694A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 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 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.585A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.756A 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 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 36 through 44 Processing helix chain 'K' and resid 58 through 69 Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.517A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.704A 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 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.278A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 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: 7.038A 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 'G' and resid 42 through 43 removed outlier: 7.277A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 27 through 28 442 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 674 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.42 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: 1.21 - 1.34: 2912 1.34 - 1.46: 4302 1.46 - 1.58: 5503 1.58 - 1.70: 575 1.70 - 1.82: 34 Bond restraints: 13326 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.46e+01 bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" C1' DA J 72 " pdb=" N9 DA J 72 " ideal model delta sigma weight residual 1.468 1.392 0.076 1.40e-02 5.10e+03 2.97e+01 bond pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.95e+01 ... (remaining 13321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 18695 2.27 - 4.54: 516 4.54 - 6.80: 25 6.80 - 9.07: 7 9.07 - 11.34: 1 Bond angle restraints: 19244 Sorted by residual: angle pdb=" N PRO K 38 " pdb=" CA PRO K 38 " pdb=" C PRO K 38 " ideal model delta sigma weight residual 113.65 102.31 11.34 1.35e+00 5.49e-01 7.06e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 108.10 5.61 9.50e-01 1.11e+00 3.48e+01 angle pdb=" O4' DC I 6 " pdb=" C4' DC I 6 " pdb=" C3' DC I 6 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 ... (remaining 19239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.48: 5746 32.48 - 64.96: 1504 64.96 - 97.44: 23 97.44 - 129.92: 3 129.92 - 162.40: 1 Dihedral angle restraints: 7277 sinusoidal: 4865 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLN G 112 " pdb=" C GLN G 112 " pdb=" N SER G 113 " pdb=" CA SER G 113 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS K 36 " pdb=" C CYS K 36 " pdb=" N LYS K 37 " pdb=" CA LYS K 37 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ASP C 90 " pdb=" C ASP C 90 " pdb=" N GLU C 91 " pdb=" CA GLU C 91 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1414 0.041 - 0.082: 522 0.082 - 0.123: 220 0.123 - 0.164: 35 0.164 - 0.205: 2 Chirality restraints: 2193 Sorted by residual: chirality pdb=" C1' DG I -70 " pdb=" O4' DG I -70 " pdb=" C2' DG I -70 " pdb=" N9 DG I -70 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS K 39 " pdb=" N CYS K 39 " pdb=" C CYS K 39 " pdb=" CB CYS K 39 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 2190 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 41 " 0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" CD GLN K 41 " -0.074 2.00e-02 2.50e+03 pdb=" OE1 GLN K 41 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN K 41 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 25 " 0.045 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO C 26 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.013 2.00e-02 2.50e+03 1.81e-02 6.55e+00 pdb=" CG TYR B 88 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.006 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 147 2.61 - 3.18: 10011 3.18 - 3.76: 22462 3.76 - 4.33: 28467 4.33 - 4.90: 41926 Nonbonded interactions: 103013 Sorted by model distance: nonbonded pdb=" CB GLU K 21 " pdb=" NH1 ARG K 91 " model vdw 2.041 3.520 nonbonded pdb=" OE2 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.106 3.120 nonbonded pdb=" OG1 THR G 16 " pdb=" OG SER G 19 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU C 64 " pdb=" OG SER K 60 " model vdw 2.159 3.040 nonbonded pdb=" N GLU D 102 " pdb=" OE1 GLU D 102 " model vdw 2.183 3.120 ... (remaining 103008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 114) selection = (chain 'G' and resid 16 through 114) } ncs_group { reference = (chain 'D' and resid 29 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=0.00 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.150 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.009 0.725 13333 Z= 0.604 Angle : 0.949 35.588 19250 Z= 0.709 Chirality : 0.049 0.205 2193 Planarity : 0.006 0.069 1434 Dihedral : 27.504 162.403 5717 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.57 % Allowed : 23.86 % Favored : 75.57 % 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: 1.52 (0.28), residues: 811 helix: 1.80 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 76 TYR 0.041 0.002 TYR B 88 PHE 0.022 0.002 PHE K 40 TRP 0.007 0.002 TRP K 61 HIS 0.010 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.56 (13326) covalent geometry : angle 0.85312 / 0.70 (19244) hydrogen bonds : bond 0.11042 / 7.47 ( 781) hydrogen bonds : angle 5.03240 / 3.51 ( 1988) metal coordination : bond 0.28246 / 14.49 ( 7) metal coordination : angle 23.53440 / 15.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 LYS cc_start: 0.8551 (mttt) cc_final: 0.8271 (mptt) REVERT: D 105 LYS cc_start: 0.8717 (tptm) cc_final: 0.8196 (mptt) REVERT: E 97 GLU cc_start: 0.8183 (tp30) cc_final: 0.7940 (tp30) REVERT: F 80 THR cc_start: 0.8982 (m) cc_final: 0.8505 (p) REVERT: G 41 GLU cc_start: 0.7839 (tp30) cc_final: 0.7634 (tp30) REVERT: G 76 THR cc_start: 0.9036 (m) cc_final: 0.8607 (t) REVERT: G 90 ASP cc_start: 0.8225 (t0) cc_final: 0.7929 (t0) REVERT: H 113 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8569 (tttm) REVERT: H 116 THR cc_start: 0.9082 (m) cc_final: 0.8674 (p) outliers start: 4 outliers final: 3 residues processed: 171 average time/residue: 0.1503 time to fit residues: 34.1371 Evaluate side-chains 159 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0030 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.062916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.050853 restraints weight = 51296.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.052155 restraints weight = 25709.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.052925 restraints weight = 16805.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053388 restraints weight = 13149.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053649 restraints weight = 11379.624| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13333 Z= 0.163 Angle : 0.689 12.230 19250 Z= 0.402 Chirality : 0.045 0.281 2193 Planarity : 0.005 0.045 1434 Dihedral : 30.084 162.085 4087 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.00 % Allowed : 23.43 % Favored : 73.57 % 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: 2.09 (0.29), residues: 811 helix: 2.21 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.79 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 99 TYR 0.046 0.002 TYR B 88 PHE 0.011 0.001 PHE K 40 TRP 0.003 0.001 TRP K 77 HIS 0.006 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (13326) covalent geometry : angle 0.67204 / 0.40 (19244) hydrogen bonds : bond 0.06012 / 4.12 ( 781) hydrogen bonds : angle 3.26616 / 2.34 ( 1988) metal coordination : bond 0.01034 / 0.69 ( 7) metal coordination : angle 8.74954 / 5.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6873 (tm-30) REVERT: D 82 LYS cc_start: 0.8491 (mttt) cc_final: 0.8194 (mptt) REVERT: D 105 LYS cc_start: 0.8720 (tptm) cc_final: 0.8180 (mptt) REVERT: F 80 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8512 (p) REVERT: G 76 THR cc_start: 0.8978 (m) cc_final: 0.8608 (t) REVERT: H 48 ASP cc_start: 0.8605 (p0) cc_final: 0.8345 (p0) REVERT: H 113 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8555 (tttm) REVERT: H 116 THR cc_start: 0.9091 (m) cc_final: 0.8721 (p) REVERT: K 41 GLN cc_start: 0.8915 (pp30) cc_final: 0.8697 (pp30) outliers start: 21 outliers final: 9 residues processed: 175 average time/residue: 0.1464 time to fit residues: 33.9160 Evaluate side-chains 164 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 13 optimal weight: 0.0570 chunk 2 optimal weight: 0.0270 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.050596 restraints weight = 52780.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.051933 restraints weight = 25902.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.052725 restraints weight = 16660.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053190 restraints weight = 12822.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053484 restraints weight = 11044.076| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13333 Z= 0.150 Angle : 0.643 20.585 19250 Z= 0.371 Chirality : 0.042 0.287 2193 Planarity : 0.005 0.051 1434 Dihedral : 30.183 164.935 4084 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 24.14 % Favored : 73.43 % 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: 811 helix: 2.35 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.039 0.002 TYR B 88 PHE 0.016 0.001 PHE C 25 TRP 0.005 0.001 TRP K 61 HIS 0.005 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (13326) covalent geometry : angle 0.60992 / 0.37 (19244) hydrogen bonds : bond 0.05449 / 3.76 ( 781) hydrogen bonds : angle 3.06586 / 2.20 ( 1988) metal coordination : bond 0.01386 / 0.93 ( 7) metal coordination : angle 11.58717 / 7.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 LYS cc_start: 0.8513 (mttt) cc_final: 0.7985 (mmtt) REVERT: D 105 LYS cc_start: 0.8719 (tptm) cc_final: 0.8150 (mptt) REVERT: D 118 TYR cc_start: 0.8689 (t80) cc_final: 0.8483 (t80) REVERT: F 80 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8540 (p) REVERT: G 76 THR cc_start: 0.8959 (m) cc_final: 0.8539 (t) REVERT: G 90 ASP cc_start: 0.8224 (t0) cc_final: 0.7965 (t70) REVERT: H 48 ASP cc_start: 0.8618 (p0) cc_final: 0.8310 (p0) REVERT: H 56 MET cc_start: 0.8713 (tpp) cc_final: 0.8484 (tpp) REVERT: H 113 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8553 (tttm) REVERT: H 116 THR cc_start: 0.9112 (m) cc_final: 0.8730 (p) REVERT: K 46 LYS cc_start: 0.8606 (pttm) cc_final: 0.8391 (ptpp) outliers start: 17 outliers final: 7 residues processed: 172 average time/residue: 0.1454 time to fit residues: 33.4485 Evaluate side-chains 163 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.048706 restraints weight = 51902.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.049966 restraints weight = 26243.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.050724 restraints weight = 17130.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.051210 restraints weight = 13322.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.051408 restraints weight = 11470.897| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13333 Z= 0.158 Angle : 0.621 9.691 19250 Z= 0.366 Chirality : 0.042 0.314 2193 Planarity : 0.004 0.040 1434 Dihedral : 30.170 165.802 4084 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.29 % Allowed : 23.29 % Favored : 73.43 % 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: 811 helix: 2.45 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -0.65 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.028 0.002 TYR B 88 PHE 0.008 0.001 PHE E 78 TRP 0.005 0.001 TRP K 61 HIS 0.003 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (13326) covalent geometry : angle 0.61027 / 0.37 (19244) hydrogen bonds : bond 0.05396 / 3.73 ( 781) hydrogen bonds : angle 3.00281 / 2.15 ( 1988) metal coordination : bond 0.02614 / 1.42 ( 7) metal coordination : angle 6.62839 / 4.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8749 (m) cc_final: 0.8225 (p) REVERT: B 92 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.6924 (ttm-80) REVERT: D 73 GLU cc_start: 0.7776 (tp30) cc_final: 0.7505 (tp30) REVERT: D 82 LYS cc_start: 0.8498 (mttt) cc_final: 0.7980 (mmtt) REVERT: D 105 LYS cc_start: 0.8698 (tptm) cc_final: 0.8124 (mptt) REVERT: F 80 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8585 (p) REVERT: G 76 THR cc_start: 0.8994 (m) cc_final: 0.8591 (t) REVERT: G 90 ASP cc_start: 0.8190 (t0) cc_final: 0.7884 (t70) REVERT: H 48 ASP cc_start: 0.8658 (p0) cc_final: 0.8385 (p0) REVERT: H 113 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8544 (tttm) REVERT: H 116 THR cc_start: 0.9113 (m) cc_final: 0.8741 (p) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.1432 time to fit residues: 32.6919 Evaluate side-chains 168 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.045520 restraints weight = 52700.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.046802 restraints weight = 25942.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047552 restraints weight = 16725.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.048034 restraints weight = 12989.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.048279 restraints weight = 11119.053| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13333 Z= 0.177 Angle : 0.640 11.313 19250 Z= 0.374 Chirality : 0.042 0.335 2193 Planarity : 0.004 0.043 1434 Dihedral : 30.220 167.289 4084 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.57 % Allowed : 24.00 % Favored : 73.43 % 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: 2.41 (0.29), residues: 811 helix: 2.47 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.032 0.002 TYR B 88 PHE 0.013 0.002 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.18 (13326) covalent geometry : angle 0.62631 / 0.37 (19244) hydrogen bonds : bond 0.05848 / 4.03 ( 781) hydrogen bonds : angle 3.02532 / 2.17 ( 1988) metal coordination : bond 0.02131 / 1.13 ( 7) metal coordination : angle 7.42833 / 3.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8807 (m) cc_final: 0.8293 (p) REVERT: B 67 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8293 (ttp80) REVERT: B 92 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6757 (ttm-80) REVERT: D 73 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: D 82 LYS cc_start: 0.8379 (mttt) cc_final: 0.7806 (mmtt) REVERT: D 105 LYS cc_start: 0.8745 (tptm) cc_final: 0.8128 (mptt) REVERT: F 80 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8652 (p) REVERT: G 76 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8639 (t) REVERT: G 90 ASP cc_start: 0.8256 (t0) cc_final: 0.7957 (t70) REVERT: H 48 ASP cc_start: 0.8666 (p0) cc_final: 0.8353 (p0) REVERT: H 49 THR cc_start: 0.9221 (m) cc_final: 0.9020 (m) REVERT: H 56 MET cc_start: 0.8700 (tpp) cc_final: 0.8487 (tpp) REVERT: H 113 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8572 (tttm) REVERT: H 116 THR cc_start: 0.9132 (m) cc_final: 0.8744 (p) outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 0.1479 time to fit residues: 31.5288 Evaluate side-chains 165 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 60 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.056121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.044468 restraints weight = 53231.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.045718 restraints weight = 26231.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.046471 restraints weight = 16973.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.046875 restraints weight = 13072.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.047186 restraints weight = 11355.366| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13333 Z= 0.163 Angle : 0.629 14.275 19250 Z= 0.366 Chirality : 0.041 0.345 2193 Planarity : 0.004 0.049 1434 Dihedral : 30.191 169.148 4084 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.57 % Allowed : 24.00 % Favored : 72.43 % 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: 2.57 (0.29), residues: 811 helix: 2.62 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.030 0.001 TYR B 88 PHE 0.011 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (13326) covalent geometry : angle 0.61253 / 0.37 (19244) hydrogen bonds : bond 0.05522 / 3.82 ( 781) hydrogen bonds : angle 2.99495 / 2.14 ( 1988) metal coordination : bond 0.01675 / 0.90 ( 7) metal coordination : angle 8.13339 / 5.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8294 (p) REVERT: B 92 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6844 (ttm-80) REVERT: D 73 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: D 82 LYS cc_start: 0.8389 (mttt) cc_final: 0.7824 (mmtt) REVERT: D 105 LYS cc_start: 0.8761 (tptm) cc_final: 0.8164 (mptt) REVERT: E 97 GLU cc_start: 0.8092 (tp30) cc_final: 0.7782 (tp30) REVERT: F 80 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8656 (p) REVERT: G 76 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8648 (t) REVERT: G 90 ASP cc_start: 0.8234 (t0) cc_final: 0.7903 (t70) REVERT: H 48 ASP cc_start: 0.8634 (p0) cc_final: 0.8364 (p0) REVERT: H 56 MET cc_start: 0.8620 (tpp) cc_final: 0.8395 (tpp) REVERT: H 113 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8587 (tttm) REVERT: H 116 THR cc_start: 0.9120 (m) cc_final: 0.8734 (p) outliers start: 25 outliers final: 13 residues processed: 166 average time/residue: 0.1460 time to fit residues: 31.8988 Evaluate side-chains 169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.042754 restraints weight = 52490.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.043984 restraints weight = 25606.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.044740 restraints weight = 16495.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.045188 restraints weight = 12680.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.045434 restraints weight = 10838.766| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13333 Z= 0.175 Angle : 0.652 18.792 19250 Z= 0.373 Chirality : 0.041 0.354 2193 Planarity : 0.004 0.056 1434 Dihedral : 30.154 169.616 4084 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.43 % Allowed : 23.57 % Favored : 73.00 % 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: 2.56 (0.29), residues: 811 helix: 2.61 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 68 TYR 0.033 0.002 TYR K 64 PHE 0.013 0.001 PHE E 78 TRP 0.003 0.001 TRP K 77 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (13326) covalent geometry : angle 0.62610 / 0.37 (19244) hydrogen bonds : bond 0.05721 / 3.96 ( 781) hydrogen bonds : angle 3.02432 / 2.16 ( 1988) metal coordination : bond 0.00623 / 0.38 ( 7) metal coordination : angle 10.38924 / 7.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.327 Fit side-chains REVERT: A 41 TYR cc_start: 0.8277 (m-80) cc_final: 0.7834 (m-10) REVERT: A 118 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 92 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.6836 (ttm-80) REVERT: D 73 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: D 82 LYS cc_start: 0.8416 (mttt) cc_final: 0.7836 (mmtt) REVERT: D 91 ILE cc_start: 0.8755 (mt) cc_final: 0.8511 (mm) REVERT: D 105 LYS cc_start: 0.8680 (tptm) cc_final: 0.8088 (mptt) REVERT: E 97 GLU cc_start: 0.8131 (tp30) cc_final: 0.7814 (tp30) REVERT: F 80 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8698 (p) REVERT: G 36 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8485 (ttmm) REVERT: G 76 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8705 (t) REVERT: G 90 ASP cc_start: 0.8275 (t0) cc_final: 0.7942 (t70) REVERT: H 48 ASP cc_start: 0.8623 (p0) cc_final: 0.8362 (p0) REVERT: H 113 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8613 (tttm) REVERT: H 116 THR cc_start: 0.9124 (m) cc_final: 0.8795 (p) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 0.1431 time to fit residues: 32.1837 Evaluate side-chains 173 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2863 r_free = 0.2863 target = 0.054554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.043131 restraints weight = 52458.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.044369 restraints weight = 25550.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.045119 restraints weight = 16482.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.045537 restraints weight = 12643.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.045832 restraints weight = 10881.581| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13333 Z= 0.146 Angle : 0.616 11.766 19250 Z= 0.362 Chirality : 0.040 0.345 2193 Planarity : 0.004 0.040 1434 Dihedral : 30.132 171.082 4084 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.86 % Allowed : 25.29 % Favored : 71.86 % 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: 2.67 (0.29), residues: 811 helix: 2.72 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 42 TYR 0.021 0.001 TYR B 88 PHE 0.009 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.003 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (13326) covalent geometry : angle 0.60438 / 0.36 (19244) hydrogen bonds : bond 0.05200 / 3.61 ( 781) hydrogen bonds : angle 2.94468 / 2.10 ( 1988) metal coordination : bond 0.00578 / 0.34 ( 7) metal coordination : angle 6.69304 / 4.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8747 (m) cc_final: 0.8345 (p) REVERT: B 92 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.6963 (ttm-80) REVERT: C 92 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 73 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: D 82 LYS cc_start: 0.8457 (mttt) cc_final: 0.7874 (mmtt) REVERT: D 90 GLU cc_start: 0.8169 (mp0) cc_final: 0.7925 (mp0) REVERT: D 91 ILE cc_start: 0.8774 (mt) cc_final: 0.8559 (mm) REVERT: D 105 LYS cc_start: 0.8759 (tptm) cc_final: 0.8191 (mptt) REVERT: E 97 GLU cc_start: 0.8086 (tp30) cc_final: 0.7765 (tp30) REVERT: F 80 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8687 (p) REVERT: G 76 THR cc_start: 0.9047 (m) cc_final: 0.8692 (t) REVERT: G 90 ASP cc_start: 0.8194 (t0) cc_final: 0.7865 (t70) REVERT: H 48 ASP cc_start: 0.8569 (p0) cc_final: 0.8292 (p0) REVERT: H 113 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8633 (tttm) REVERT: H 116 THR cc_start: 0.9166 (m) cc_final: 0.8788 (p) outliers start: 20 outliers final: 14 residues processed: 169 average time/residue: 0.1469 time to fit residues: 33.2254 Evaluate side-chains 172 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.2860 r_free = 0.2860 target = 0.054392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.043068 restraints weight = 52826.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.044308 restraints weight = 25678.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.045043 restraints weight = 16460.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.045496 restraints weight = 12663.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.045615 restraints weight = 10849.274| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13333 Z= 0.146 Angle : 0.625 14.834 19250 Z= 0.363 Chirality : 0.040 0.344 2193 Planarity : 0.004 0.040 1434 Dihedral : 30.062 170.824 4084 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.14 % Allowed : 25.00 % Favored : 71.86 % 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: 2.71 (0.29), residues: 811 helix: 2.72 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 42 TYR 0.023 0.002 TYR B 88 PHE 0.008 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (13326) covalent geometry : angle 0.61316 / 0.36 (19244) hydrogen bonds : bond 0.05091 / 3.54 ( 781) hydrogen bonds : angle 2.91951 / 2.08 ( 1988) metal coordination : bond 0.00512 / 0.30 ( 7) metal coordination : angle 6.87374 / 4.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8325 (m-80) cc_final: 0.7767 (m-10) REVERT: A 118 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8319 (p) REVERT: B 92 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.6995 (ttm-80) REVERT: D 73 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: D 82 LYS cc_start: 0.8437 (mttt) cc_final: 0.7848 (mmtt) REVERT: D 90 GLU cc_start: 0.8156 (mp0) cc_final: 0.7923 (mp0) REVERT: D 91 ILE cc_start: 0.8777 (mt) cc_final: 0.8564 (mm) REVERT: D 105 LYS cc_start: 0.8660 (tptm) cc_final: 0.8150 (mptt) REVERT: E 42 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7730 (mmm-85) REVERT: E 97 GLU cc_start: 0.8114 (tp30) cc_final: 0.7803 (tp30) REVERT: F 80 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8680 (p) REVERT: G 36 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8520 (ttmm) REVERT: G 76 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8680 (t) REVERT: G 90 ASP cc_start: 0.8218 (t0) cc_final: 0.7871 (t70) REVERT: H 48 ASP cc_start: 0.8544 (p0) cc_final: 0.8278 (p0) REVERT: H 113 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8629 (tttm) REVERT: H 116 THR cc_start: 0.9159 (m) cc_final: 0.8784 (p) REVERT: K 46 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7777 (pttm) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 0.1500 time to fit residues: 33.8901 Evaluate side-chains 175 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.052574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.041418 restraints weight = 52878.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.042590 restraints weight = 26878.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.043286 restraints weight = 17686.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.043736 restraints weight = 13795.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.044000 restraints weight = 11831.604| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13333 Z= 0.165 Angle : 0.643 11.537 19250 Z= 0.373 Chirality : 0.041 0.354 2193 Planarity : 0.005 0.099 1434 Dihedral : 30.029 170.462 4084 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.00 % Allowed : 25.86 % Favored : 71.14 % 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: 811 helix: 2.61 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 42 TYR 0.019 0.001 TYR B 88 PHE 0.011 0.001 PHE E 78 TRP 0.003 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (13326) covalent geometry : angle 0.63411 / 0.37 (19244) hydrogen bonds : bond 0.05535 / 3.82 ( 781) hydrogen bonds : angle 2.98945 / 2.12 ( 1988) metal coordination : bond 0.00419 / 0.23 ( 7) metal coordination : angle 5.99579 / 3.72 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8153 (m-80) cc_final: 0.7940 (m-10) REVERT: A 118 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8351 (p) REVERT: B 92 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7122 (ttm-80) REVERT: D 73 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: D 82 LYS cc_start: 0.8398 (mttt) cc_final: 0.7847 (mmtt) REVERT: D 90 GLU cc_start: 0.8185 (mp0) cc_final: 0.7941 (mp0) REVERT: D 91 ILE cc_start: 0.8789 (mt) cc_final: 0.8564 (mm) REVERT: D 105 LYS cc_start: 0.8743 (tptm) cc_final: 0.8180 (mptt) REVERT: F 80 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8655 (p) REVERT: G 35 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8234 (ttm-80) REVERT: G 36 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8490 (ttmm) REVERT: G 76 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8694 (t) REVERT: G 90 ASP cc_start: 0.8178 (t0) cc_final: 0.7881 (t70) REVERT: H 48 ASP cc_start: 0.8514 (p0) cc_final: 0.8223 (p0) REVERT: H 113 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8620 (tttm) REVERT: H 116 THR cc_start: 0.9157 (m) cc_final: 0.8795 (p) outliers start: 21 outliers final: 15 residues processed: 171 average time/residue: 0.1406 time to fit residues: 32.2872 Evaluate side-chains 176 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 19 optimal weight: 0.0670 chunk 25 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.054071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.043042 restraints weight = 52668.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.044211 restraints weight = 26511.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.044915 restraints weight = 17339.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.045360 restraints weight = 13456.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.045583 restraints weight = 11562.593| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13333 Z= 0.139 Angle : 0.615 11.365 19250 Z= 0.361 Chirality : 0.040 0.333 2193 Planarity : 0.005 0.094 1434 Dihedral : 30.000 172.038 4084 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.00 % Allowed : 25.14 % Favored : 71.86 % 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: 2.71 (0.29), residues: 811 helix: 2.71 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 42 TYR 0.018 0.001 TYR D 80 PHE 0.006 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.003 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (13326) covalent geometry : angle 0.60669 / 0.36 (19244) hydrogen bonds : bond 0.04818 / 3.37 ( 781) hydrogen bonds : angle 2.93464 / 2.08 ( 1988) metal coordination : bond 0.00348 / 0.19 ( 7) metal coordination : angle 5.81229 / 3.63 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.69 seconds wall clock time: 34 minutes 14.45 seconds (2054.45 seconds total)