Starting phenix.real_space_refine on Thu Aug 6 00:46:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kq2_62494/08_2026/9kq2_62494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kq2_62494/08_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_62494/08_2026/9kq2_62494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kq2_62494/08_2026/9kq2_62494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kq2_62494/08_2026/9kq2_62494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kq2_62494/08_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-2.2rc3-6140/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: 2.24, per 1000 atoms: 0.18 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: 0.81 Conformation dependent library (CDL) restraints added in 293.1 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: 1.57 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: 2.16 Time building geometry restraints manager: 1.08 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: 18692 2.27 - 4.54: 519 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: 1.410 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.670 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- 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 : 0.953 35.588 19250 Z= 0.713 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 0.85772 / 0.71 (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 : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 LYS cc_start: 0.8551 (mttt) cc_final: 0.8267 (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: 0.7633 (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: 0.7931 (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: 0.1196 time to fit residues: 27.4139 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 : 0.246 ------------------------------------------------------------------------------- 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: 0.6980 chunk 100 optimal weight: 0.0030 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.063079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.051003 restraints weight = 51210.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052305 restraints weight = 25636.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.053084 restraints weight = 16794.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.053534 restraints weight = 13064.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.053797 restraints weight = 11354.958| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2796 r_free = 0.2796 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: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1148 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= 0.160 Angle : 0.695 13.413 19250 Z= 0.401 Chirality : 0.045 0.296 2193 Planarity : 0.005 0.045 1434 Dihedral : 29.985 161.189 4087 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.00 % Allowed : 23.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.29), residues: 811 helix: 2.20 (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 0.047 0.002 TYR B 88 PHE 0.008 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 0.00260 / 0.16 (13326) covalent geometry : angle 0.67442 / 0.40 (19244) hydrogen bonds : bond 0.05988 / 4.10 ( 781) hydrogen bonds : angle 3.28186 / 2.35 ( 1988) metal coordination : bond 0.00642 / 0.41 ( 7) metal coordination : angle 9.59894 / 6.11 ( 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 : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7300 (p) REVERT: C 92 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7051 (tm-30) REVERT: D 82 LYS cc_start: 0.8467 (mttt) cc_final: 0.8190 (mptt) REVERT: D 105 LYS cc_start: 0.8717 (tptm) cc_final: 0.8182 (mptt) REVERT: F 80 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8508 (p) REVERT: G 76 THR cc_start: 0.8983 (m) cc_final: 0.8607 (t) REVERT: G 90 ASP cc_start: 0.8033 (t0) cc_final: 0.7703 (t0) REVERT: H 48 ASP cc_start: 0.8593 (p0) cc_final: 0.8353 (p0) REVERT: H 113 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8556 (tttm) REVERT: H 116 THR cc_start: 0.9089 (m) cc_final: 0.8719 (p) REVERT: K 41 GLN cc_start: 0.8940 (pp30) cc_final: 0.8652 (pp30) REVERT: K 46 LYS cc_start: 0.8588 (pttm) cc_final: 0.8228 (pttm) outliers start: 21 outliers final: 9 residues processed: 176 average time/residue: 0.1188 time to fit residues: 27.8839 Evaluate side-chains 166 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR 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 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: 0.1980 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.059915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.047981 restraints weight = 53082.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049293 restraints weight = 25933.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.050080 restraints weight = 16622.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.050584 restraints weight = 12788.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050821 restraints weight = 10895.674| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13333 Z= 0.171 Angle : 0.691 20.557 19250 Z= 0.388 Chirality : 0.043 0.315 2193 Planarity : 0.005 0.054 1434 Dihedral : 30.174 162.525 4084 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 24.29 % 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: 2.24 (0.29), residues: 811 helix: 2.31 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.73 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 99 TYR 0.037 0.002 TYR B 88 PHE 0.009 0.001 PHE E 78 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 0.00304 / 0.17 (13326) covalent geometry : angle 0.65356 / 0.39 (19244) hydrogen bonds : bond 0.06033 / 4.15 ( 781) hydrogen bonds : angle 3.14950 / 2.26 ( 1988) metal coordination : bond 0.02500 / 1.53 ( 7) metal coordination : angle 12.79200 / 7.64 ( 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 178 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 82 LYS cc_start: 0.8444 (mttt) cc_final: 0.7860 (mmtt) REVERT: D 105 LYS cc_start: 0.8750 (tptm) cc_final: 0.8151 (mptt) REVERT: F 80 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8562 (p) REVERT: G 76 THR cc_start: 0.9011 (m) cc_final: 0.8589 (t) REVERT: G 90 ASP cc_start: 0.8078 (t0) cc_final: 0.7727 (t0) REVERT: H 48 ASP cc_start: 0.8650 (p0) cc_final: 0.8361 (p0) REVERT: H 56 MET cc_start: 0.8696 (tpp) cc_final: 0.8482 (tpp) REVERT: H 113 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8551 (tttm) REVERT: H 116 THR cc_start: 0.9133 (m) cc_final: 0.8739 (p) REVERT: K 41 GLN cc_start: 0.9038 (pp30) cc_final: 0.8781 (pp30) outliers start: 19 outliers final: 10 residues processed: 172 average time/residue: 0.1472 time to fit residues: 33.9784 Evaluate side-chains 168 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 D residue 86 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain K residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.2968 r_free = 0.2968 target = 0.059161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.047411 restraints weight = 52501.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.048657 restraints weight = 26294.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.049408 restraints weight = 17200.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.049827 restraints weight = 13347.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.050133 restraints weight = 11590.713| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13333 Z= 0.154 Angle : 0.633 9.701 19250 Z= 0.370 Chirality : 0.042 0.337 2193 Planarity : 0.004 0.041 1434 Dihedral : 30.158 165.137 4084 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 24.29 % Favored : 73.14 % 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: 2.48 (0.29), residues: 811 helix: 2.53 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.032 0.002 TYR B 88 PHE 0.009 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (13326) covalent geometry : angle 0.62348 / 0.37 (19244) hydrogen bonds : bond 0.05442 / 3.76 ( 781) hydrogen bonds : angle 3.00652 / 2.15 ( 1988) metal coordination : bond 0.01853 / 1.25 ( 7) metal coordination : angle 6.19525 / 4.28 ( 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 177 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8789 (m) cc_final: 0.8254 (p) REVERT: B 92 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7033 (ttm-80) REVERT: D 73 GLU cc_start: 0.7328 (tp30) cc_final: 0.7017 (tp30) REVERT: D 82 LYS cc_start: 0.8382 (mttt) cc_final: 0.7830 (mmtt) REVERT: D 105 LYS cc_start: 0.8716 (tptm) cc_final: 0.8138 (mptt) REVERT: E 97 GLU cc_start: 0.8044 (tp30) cc_final: 0.7762 (tp30) REVERT: F 80 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8603 (p) REVERT: G 76 THR cc_start: 0.9016 (m) cc_final: 0.8608 (t) REVERT: G 90 ASP cc_start: 0.8068 (t0) cc_final: 0.7718 (t0) REVERT: H 48 ASP cc_start: 0.8660 (p0) cc_final: 0.8391 (p0) REVERT: H 56 MET cc_start: 0.8697 (tpp) cc_final: 0.8476 (tpp) REVERT: H 113 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8578 (tttm) REVERT: H 116 THR cc_start: 0.9130 (m) cc_final: 0.8755 (p) REVERT: K 46 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (pttm) outliers start: 18 outliers final: 9 residues processed: 168 average time/residue: 0.1585 time to fit residues: 35.1342 Evaluate side-chains 167 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 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 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 K residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.056133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.044529 restraints weight = 52552.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.045730 restraints weight = 26650.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.046455 restraints weight = 17634.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.046817 restraints weight = 13730.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.047148 restraints weight = 12060.723| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13333 Z= 0.171 Angle : 0.661 14.587 19250 Z= 0.377 Chirality : 0.042 0.361 2193 Planarity : 0.005 0.041 1434 Dihedral : 30.147 165.383 4084 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.43 % Allowed : 23.14 % 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: 2.37 (0.29), residues: 811 helix: 2.43 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 35 TYR 0.035 0.002 TYR B 88 PHE 0.016 0.002 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (13326) covalent geometry : angle 0.64032 / 0.38 (19244) hydrogen bonds : bond 0.06051 / 4.15 ( 781) hydrogen bonds : angle 3.03172 / 2.17 ( 1988) metal coordination : bond 0.00885 / 0.44 ( 7) metal coordination : angle 9.23449 / 4.89 ( 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 183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7007 (ttm-80) REVERT: D 82 LYS cc_start: 0.8418 (mttt) cc_final: 0.7841 (mmtt) REVERT: D 97 LEU cc_start: 0.8695 (mt) cc_final: 0.8453 (mt) REVERT: D 105 LYS cc_start: 0.8757 (tptm) cc_final: 0.8162 (mptt) REVERT: F 80 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8624 (p) REVERT: G 38 ASN cc_start: 0.8499 (m-40) cc_final: 0.8106 (m-40) REVERT: G 76 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8642 (t) REVERT: G 90 ASP cc_start: 0.8129 (t0) cc_final: 0.7804 (t70) REVERT: H 48 ASP cc_start: 0.8626 (p0) cc_final: 0.8307 (p0) REVERT: H 49 THR cc_start: 0.9216 (m) cc_final: 0.9007 (m) REVERT: H 113 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8577 (tttm) REVERT: H 116 THR cc_start: 0.9121 (m) cc_final: 0.8740 (p) outliers start: 24 outliers final: 17 residues processed: 171 average time/residue: 0.1534 time to fit residues: 34.9151 Evaluate side-chains 175 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 53 SER 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 Chi-restraints excluded: chain H residue 31 LYS 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: 0.7980 chunk 70 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.2888 r_free = 0.2888 target = 0.055700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.044168 restraints weight = 52708.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.045372 restraints weight = 26595.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.046093 restraints weight = 17406.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.046479 restraints weight = 13567.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.046790 restraints weight = 11803.602| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 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 = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13333 Z= 0.153 Angle : 0.789 42.660 19250 Z= 0.376 Chirality : 0.041 0.364 2193 Planarity : 0.004 0.040 1434 Dihedral : 30.130 168.416 4084 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 24.71 % Favored : 72.57 % 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: 2.56 (0.29), residues: 811 helix: 2.62 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.82 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.025 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 0.00257 / 0.15 (13326) covalent geometry : angle 0.61903 / 0.37 (19244) hydrogen bonds : bond 0.05422 / 3.76 ( 781) hydrogen bonds : angle 2.98904 / 2.13 ( 1988) metal coordination : bond 0.01092 / 0.58 ( 7) metal coordination : angle 27.74860 / 17.42 ( 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: 19 poor density : 161 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7010 (ttm-80) REVERT: D 82 LYS cc_start: 0.8405 (mttt) cc_final: 0.7825 (mmtt) REVERT: D 97 LEU cc_start: 0.8652 (mt) cc_final: 0.8398 (mt) REVERT: D 105 LYS cc_start: 0.8744 (tptm) cc_final: 0.8173 (mptt) REVERT: E 97 GLU cc_start: 0.8038 (tp30) cc_final: 0.7759 (tp30) REVERT: F 80 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8625 (p) REVERT: G 76 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8642 (t) REVERT: G 90 ASP cc_start: 0.8120 (t0) cc_final: 0.7783 (t0) REVERT: H 48 ASP cc_start: 0.8615 (p0) cc_final: 0.8328 (p0) REVERT: H 49 THR cc_start: 0.9234 (m) cc_final: 0.9027 (m) REVERT: H 113 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8610 (tttm) REVERT: H 116 THR cc_start: 0.9124 (m) cc_final: 0.8749 (p) outliers start: 19 outliers final: 11 residues processed: 170 average time/residue: 0.1629 time to fit residues: 36.4500 Evaluate side-chains 167 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 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 16 THR 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 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 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: 1.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.2879 r_free = 0.2879 target = 0.055249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.043774 restraints weight = 52840.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.045016 restraints weight = 25676.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.045772 restraints weight = 16504.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.046205 restraints weight = 12644.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.046512 restraints weight = 10840.737| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13333 Z= 0.149 Angle : 0.645 17.692 19250 Z= 0.368 Chirality : 0.041 0.367 2193 Planarity : 0.004 0.053 1434 Dihedral : 30.066 168.108 4084 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.57 % Allowed : 25.14 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.29), residues: 811 helix: 2.62 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.029 0.001 TYR B 88 PHE 0.010 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 0.00250 / 0.15 (13326) covalent geometry : angle 0.62148 / 0.37 (19244) hydrogen bonds : bond 0.05291 / 3.66 ( 781) hydrogen bonds : angle 2.95739 / 2.11 ( 1988) metal coordination : bond 0.01261 / 0.75 ( 7) metal coordination : angle 9.81677 / 5.97 ( 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 183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7040 (ttm-80) REVERT: D 82 LYS cc_start: 0.8364 (mttt) cc_final: 0.7814 (mmtt) REVERT: D 97 LEU cc_start: 0.8609 (mt) cc_final: 0.8365 (mt) REVERT: D 105 LYS cc_start: 0.8728 (tptm) cc_final: 0.8138 (mptt) REVERT: F 77 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: F 80 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8654 (p) REVERT: G 36 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8496 (ttmm) REVERT: G 76 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8649 (t) REVERT: G 90 ASP cc_start: 0.8137 (t0) cc_final: 0.7764 (t0) REVERT: H 48 ASP cc_start: 0.8642 (p0) cc_final: 0.8354 (p0) REVERT: H 56 MET cc_start: 0.8619 (tpp) cc_final: 0.8392 (tpp) REVERT: H 113 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8625 (tttm) REVERT: H 116 THR cc_start: 0.9123 (m) cc_final: 0.8788 (p) outliers start: 18 outliers final: 11 residues processed: 173 average time/residue: 0.1610 time to fit residues: 36.5937 Evaluate side-chains 172 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 86 ILE 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 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: 5.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 95 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.2885 r_free = 0.2885 target = 0.055400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.044018 restraints weight = 52745.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.045302 restraints weight = 25675.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.046060 restraints weight = 16281.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.046475 restraints weight = 12410.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.046800 restraints weight = 10708.794| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13333 Z= 0.141 Angle : 0.653 23.322 19250 Z= 0.366 Chirality : 0.040 0.361 2193 Planarity : 0.004 0.039 1434 Dihedral : 30.009 169.294 4084 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 25.71 % Favored : 71.57 % 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: 2.64 (0.29), residues: 811 helix: 2.70 (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 0.011 0.001 ARG E 42 TYR 0.023 0.001 TYR B 88 PHE 0.008 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (13326) covalent geometry : angle 0.62114 / 0.36 (19244) hydrogen bonds : bond 0.04929 / 3.45 ( 781) hydrogen bonds : angle 2.92543 / 2.08 ( 1988) metal coordination : bond 0.00849 / 0.49 ( 7) metal coordination : angle 11.44262 / 7.23 ( 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 182 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 92 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7054 (ttm-80) REVERT: D 82 LYS cc_start: 0.8398 (mttt) cc_final: 0.7816 (mmtt) REVERT: D 97 LEU cc_start: 0.8594 (mt) cc_final: 0.8327 (mt) REVERT: D 105 LYS cc_start: 0.8786 (tptm) cc_final: 0.8189 (mptt) REVERT: E 97 GLU cc_start: 0.8116 (tp30) cc_final: 0.7817 (tp30) REVERT: F 80 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8652 (p) REVERT: G 76 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8666 (t) REVERT: G 90 ASP cc_start: 0.8140 (t0) cc_final: 0.7811 (t0) REVERT: H 48 ASP cc_start: 0.8558 (p0) cc_final: 0.8306 (p0) REVERT: H 56 MET cc_start: 0.8612 (tpp) cc_final: 0.8360 (tpp) REVERT: H 113 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8614 (tttm) REVERT: H 116 THR cc_start: 0.9161 (m) cc_final: 0.8783 (p) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 0.1573 time to fit residues: 35.8600 Evaluate side-chains 176 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 86 ILE 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 Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.2840 r_free = 0.2840 target = 0.053637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.042453 restraints weight = 53136.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.043643 restraints weight = 26802.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.044347 restraints weight = 17504.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.044749 restraints weight = 13619.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.045038 restraints weight = 11773.660| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 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 = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13333 Z= 0.157 Angle : 0.647 14.215 19250 Z= 0.371 Chirality : 0.041 0.371 2193 Planarity : 0.004 0.054 1434 Dihedral : 29.960 167.838 4084 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.14 % Allowed : 26.29 % Favored : 70.57 % 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: 2.62 (0.29), residues: 811 helix: 2.67 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 99 TYR 0.023 0.002 TYR K 64 PHE 0.011 0.001 PHE E 78 TRP 0.004 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (13326) covalent geometry : angle 0.63322 / 0.37 (19244) hydrogen bonds : bond 0.05366 / 3.71 ( 781) hydrogen bonds : angle 2.97385 / 2.13 ( 1988) metal coordination : bond 0.00760 / 0.41 ( 7) metal coordination : angle 7.61353 / 4.59 ( 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 182 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 92 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7034 (ttm-80) REVERT: D 82 LYS cc_start: 0.8467 (mttt) cc_final: 0.7910 (mmtt) REVERT: D 97 LEU cc_start: 0.8620 (mt) cc_final: 0.8395 (mt) REVERT: D 102 GLU cc_start: 0.7210 (mp0) cc_final: 0.6894 (mm-30) REVERT: D 105 LYS cc_start: 0.8840 (tptm) cc_final: 0.8314 (mptt) REVERT: E 97 GLU cc_start: 0.8089 (tp30) cc_final: 0.7799 (tp30) REVERT: F 77 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: F 80 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8639 (p) REVERT: G 36 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8545 (ttmm) REVERT: G 76 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8681 (t) REVERT: G 90 ASP cc_start: 0.8172 (t0) cc_final: 0.7864 (t70) REVERT: H 48 ASP cc_start: 0.8494 (p0) cc_final: 0.8213 (p0) REVERT: H 56 MET cc_start: 0.8672 (tpp) cc_final: 0.8386 (tpp) REVERT: H 113 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8615 (tttm) REVERT: H 116 THR cc_start: 0.9160 (m) cc_final: 0.8799 (p) outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 0.1399 time to fit residues: 32.1737 Evaluate side-chains 177 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 29 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.053357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.042210 restraints weight = 53200.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.043405 restraints weight = 27044.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.044124 restraints weight = 17650.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.044569 restraints weight = 13671.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.044744 restraints weight = 11727.263| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 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 = 0.2571 r_free = 0.2571 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 (11 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13333 Z= 0.148 Angle : 0.643 16.756 19250 Z= 0.367 Chirality : 0.041 0.368 2193 Planarity : 0.004 0.040 1434 Dihedral : 29.972 169.270 4084 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 25.57 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.29), residues: 811 helix: 2.70 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 76 TYR 0.023 0.001 TYR D 37 PHE 0.009 0.001 PHE E 78 TRP 0.005 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (13326) covalent geometry : angle 0.62630 / 0.37 (19244) hydrogen bonds : bond 0.05132 / 3.56 ( 781) hydrogen bonds : angle 2.95663 / 2.11 ( 1988) metal coordination : bond 0.00637 / 0.35 ( 7) metal coordination : angle 8.18352 / 4.96 ( 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 179 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 92 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7083 (ttm-80) REVERT: D 82 LYS cc_start: 0.8429 (mttt) cc_final: 0.7880 (mmtt) REVERT: D 97 LEU cc_start: 0.8617 (mt) cc_final: 0.8396 (mt) REVERT: D 105 LYS cc_start: 0.8820 (tptm) cc_final: 0.8291 (mptt) REVERT: E 97 GLU cc_start: 0.8081 (tp30) cc_final: 0.7794 (tp30) REVERT: F 77 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: F 80 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8636 (p) REVERT: G 36 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8482 (ttmm) REVERT: G 76 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8681 (t) REVERT: G 90 ASP cc_start: 0.8171 (t0) cc_final: 0.7864 (t0) REVERT: H 48 ASP cc_start: 0.8552 (p0) cc_final: 0.8275 (p0) REVERT: H 113 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8607 (tttm) REVERT: H 116 THR cc_start: 0.9157 (m) cc_final: 0.8799 (p) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.1484 time to fit residues: 33.2274 Evaluate side-chains 177 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 86 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 29 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 G residue 111 ILE 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: 2.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.046983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.036070 restraints weight = 53104.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.037166 restraints weight = 27469.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.037827 restraints weight = 18244.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.038233 restraints weight = 14253.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.038448 restraints weight = 12331.840| |-----------------------------------------------------------------------------| r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13333 Z= 0.250 Angle : 0.820 14.653 19250 Z= 0.450 Chirality : 0.050 0.412 2193 Planarity : 0.006 0.056 1434 Dihedral : 30.116 166.631 4084 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.57 % Allowed : 25.00 % Favored : 71.43 % 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: 1.72 (0.28), residues: 811 helix: 1.98 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.03 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.030 0.002 TYR B 88 PHE 0.021 0.003 PHE K 53 TRP 0.004 0.001 TRP K 61 HIS 0.006 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 (13326) covalent geometry : angle 0.80727 / 0.45 (19244) hydrogen bonds : bond 0.08222 / 5.61 ( 781) hydrogen bonds : angle 3.45872 / 2.49 ( 1988) metal coordination : bond 0.00656 / 0.34 ( 7) metal coordination : angle 8.25017 / 5.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.04 seconds wall clock time: 33 minutes 45.36 seconds (2025.36 seconds total)