Starting phenix.real_space_refine on Wed Aug 5 13:51:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.map" model { file = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2026/8uba_42080.cif" } resolution = 3.2 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= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 37 5.16 5 C 6036 2.51 5 N 1861 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 10299 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 893 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2481 Classifications: {'RNA': 116} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 17, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10299 At special positions: 0 Unit cell: (84, 100, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 143 15.00 O 2222 8.00 N 1861 7.00 C 6036 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: 0.87 Conformation dependent library (CDL) restraints added in 270.0 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 75.0% alpha, 2.9% beta 46 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 4.259A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.522A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.773A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.911A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.558A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.857A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'B' and resid 10 through 33 removed outlier: 3.634A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.404A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 11 through 34 removed outlier: 3.653A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 50 through 62 removed outlier: 4.389A pdb=" N GLU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.591A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.713A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.568A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.934A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 123 removed outlier: 4.030A pdb=" N GLN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.639A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 28 removed outlier: 3.788A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.867A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.304A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.839A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 487 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1948 1.33 - 1.46: 4266 1.46 - 1.59: 4279 1.59 - 1.72: 265 1.72 - 1.85: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CG HIS E 38 " pdb=" CD2 HIS E 38 " ideal model delta sigma weight residual 1.354 1.276 0.078 1.10e-02 8.26e+03 4.99e+01 bond pdb=" CE1 HIS E 38 " pdb=" NE2 HIS E 38 " ideal model delta sigma weight residual 1.321 1.257 0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 1.530 1.630 -0.099 1.69e-02 3.50e+03 3.45e+01 bond pdb=" CA GLU F 100 " pdb=" CB GLU F 100 " ideal model delta sigma weight residual 1.529 1.608 -0.079 1.58e-02 4.01e+03 2.52e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.535 1.609 -0.074 1.51e-02 4.39e+03 2.39e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14035 2.11 - 4.21: 1135 4.21 - 6.32: 115 6.32 - 8.42: 25 8.42 - 10.53: 6 Bond angle restraints: 15316 Sorted by residual: angle pdb=" C3' U I 67 " pdb=" O3' U I 67 " pdb=" P C I 68 " ideal model delta sigma weight residual 119.70 110.57 9.13 1.20e+00 6.94e-01 5.78e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 119.70 111.20 8.50 1.20e+00 6.94e-01 5.02e+01 angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 96.08 7.17 1.05e+00 9.07e-01 4.66e+01 angle pdb=" C3' U I 120 " pdb=" O3' U I 120 " pdb=" P G I 121 " ideal model delta sigma weight residual 119.70 111.70 8.00 1.20e+00 6.94e-01 4.45e+01 angle pdb=" C3' U I 7 " pdb=" O3' U I 7 " pdb=" P C I 8 " ideal model delta sigma weight residual 119.70 112.11 7.59 1.20e+00 6.94e-01 4.00e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 6009 35.39 - 70.77: 637 70.77 - 106.16: 62 106.16 - 141.55: 1 141.55 - 176.93: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 55.07 176.93 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -91.97 -68.03 1 1.50e+01 4.44e-03 2.67e+01 dihedral pdb=" CA LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " pdb=" CA PRO D 91 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 1584 0.137 - 0.273: 213 0.273 - 0.410: 5 0.410 - 0.547: 9 0.547 - 0.683: 2 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.09 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.063 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR C 28 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " 0.063 2.00e-02 2.50e+03 3.12e-02 2.20e+01 pdb=" N1 U I 7 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U I 7 " -0.031 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U I 7 " -0.018 2.00e-02 2.50e+03 pdb=" C4 U I 7 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U I 7 " 0.035 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U I 7 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 28 " -0.041 2.00e-02 2.50e+03 3.02e-02 1.83e+01 pdb=" CG TYR E 28 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 28 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 28 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 28 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR E 28 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 28 " -0.049 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1317 2.74 - 3.28: 10909 3.28 - 3.82: 21452 3.82 - 4.36: 26920 4.36 - 4.90: 38269 Nonbonded interactions: 98867 Sorted by model distance: nonbonded pdb=" NZ LYS A 3 " pdb=" N7 G I 108 " model vdw 2.202 3.200 nonbonded pdb=" OH TYR A 152 " pdb=" O LEU A 168 " model vdw 2.230 3.040 nonbonded pdb=" O LYS A 113 " pdb=" O2' C H 120 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 264 " pdb=" O LEU A 272 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR A 152 " pdb=" O LEU A 172 " model vdw 2.261 3.040 ... (remaining 98862 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 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.011 0.129 10820 Z= 0.690 Angle : 1.239 10.528 15316 Z= 0.844 Chirality : 0.095 0.683 1813 Planarity : 0.010 0.087 1402 Dihedral : 23.380 176.931 5028 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 2.03 % Allowed : 8.25 % Favored : 89.72 % Rotamer: Outliers : 7.20 % Allowed : 14.67 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.23), residues: 885 helix: -1.84 (0.16), residues: 648 sheet: -4.28 (0.74), residues: 24 loop : -3.93 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG A 208 TYR 0.063 0.009 TYR C 28 PHE 0.035 0.008 PHE A 98 TRP 0.044 0.009 TRP A 15 HIS 0.016 0.003 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.01084 / 0.69 (10820) covalent geometry : angle 1.23880 / 0.84 (15316) hydrogen bonds : bond 0.20613 / 13.34 ( 607) hydrogen bonds : angle 8.91615 / 6.16 ( 1628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7437 (ptp-110) REVERT: A 16 GLU cc_start: 0.8875 (mp0) cc_final: 0.8267 (tm-30) REVERT: A 24 LYS cc_start: 0.8314 (mttp) cc_final: 0.7957 (mtmt) REVERT: A 68 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 70 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 116 HIS cc_start: 0.7549 (t70) cc_final: 0.7193 (m90) REVERT: A 141 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7793 (mtmm) REVERT: A 161 CYS cc_start: 0.8944 (t) cc_final: 0.8532 (t) REVERT: B 25 SER cc_start: 0.9399 (t) cc_final: 0.9144 (p) REVERT: B 90 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7475 (mttt) REVERT: C 14 MET cc_start: 0.7722 (tpt) cc_final: 0.7260 (mtt) REVERT: C 40 VAL cc_start: 0.9047 (t) cc_final: 0.8807 (t) REVERT: C 67 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8335 (mmtm) REVERT: C 117 ILE cc_start: 0.8584 (mt) cc_final: 0.8347 (mt) REVERT: C 121 ASN cc_start: 0.8277 (m-40) cc_final: 0.8050 (m-40) REVERT: D 21 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8082 (mm-30) REVERT: D 26 TYR cc_start: 0.8455 (t80) cc_final: 0.7418 (t80) REVERT: D 37 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7519 (ptmt) REVERT: D 44 MET cc_start: 0.8500 (mtp) cc_final: 0.8288 (mtt) REVERT: D 69 TYR cc_start: 0.8095 (m-80) cc_final: 0.7878 (m-80) REVERT: D 98 GLN cc_start: 0.8439 (mt0) cc_final: 0.8098 (mt0) REVERT: E 14 MET cc_start: 0.6281 (tpp) cc_final: 0.5836 (tpp) REVERT: E 64 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: E 79 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7870 (mtt-85) REVERT: E 98 GLN cc_start: 0.8233 (mt0) cc_final: 0.7905 (mt0) REVERT: E 111 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8283 (ptt90) REVERT: F 14 MET cc_start: 0.6758 (mmt) cc_final: 0.5790 (tmm) REVERT: F 19 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7903 (mmm160) REVERT: F 26 TYR cc_start: 0.8473 (t80) cc_final: 0.8178 (t80) REVERT: F 43 GLU cc_start: 0.8488 (tt0) cc_final: 0.7889 (mt-10) REVERT: F 89 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: F 95 THR cc_start: 0.7945 (p) cc_final: 0.7629 (t) outliers start: 54 outliers final: 14 residues processed: 278 average time/residue: 0.1437 time to fit residues: 51.5666 Evaluate side-chains 211 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 92 HIS C 89 GLN C 92 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN F 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118486 restraints weight = 15713.166| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.72 r_work: 0.3401 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10820 Z= 0.218 Angle : 0.757 13.741 15316 Z= 0.401 Chirality : 0.046 0.243 1813 Planarity : 0.008 0.162 1402 Dihedral : 23.880 178.274 3315 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.76 % Favored : 93.33 % Rotamer: Outliers : 5.87 % Allowed : 16.27 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -2.19 (0.26), residues: 885 helix: -0.70 (0.18), residues: 661 sheet: -4.03 (0.73), residues: 26 loop : -3.27 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.023 0.003 TYR D 26 PHE 0.021 0.003 PHE A 231 TRP 0.011 0.002 TRP C 81 HIS 0.006 0.002 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (10820) covalent geometry : angle 0.75715 / 0.40 (15316) hydrogen bonds : bond 0.07716 / 5.04 ( 607) hydrogen bonds : angle 5.19518 / 3.63 ( 1628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6862 (mpt-90) REVERT: A 68 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 161 CYS cc_start: 0.8410 (t) cc_final: 0.8159 (t) REVERT: A 164 THR cc_start: 0.8389 (m) cc_final: 0.8142 (m) REVERT: A 184 LEU cc_start: 0.8723 (tp) cc_final: 0.8340 (tp) REVERT: B 90 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7096 (mttp) REVERT: C 89 GLN cc_start: 0.7404 (tt0) cc_final: 0.7052 (tm-30) REVERT: D 37 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7804 (ttmm) REVERT: D 89 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: D 108 GLU cc_start: 0.7776 (tp30) cc_final: 0.7121 (tp30) REVERT: E 14 MET cc_start: 0.6700 (tpp) cc_final: 0.6218 (tpp) REVERT: E 54 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: F 14 MET cc_start: 0.6578 (mmt) cc_final: 0.6016 (tmm) REVERT: F 19 ARG cc_start: 0.7455 (mmm160) cc_final: 0.6679 (mmm160) REVERT: F 43 GLU cc_start: 0.8119 (tt0) cc_final: 0.7382 (mt-10) outliers start: 44 outliers final: 15 residues processed: 235 average time/residue: 0.1069 time to fit residues: 33.8365 Evaluate side-chains 199 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 32 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118865 restraints weight = 15836.407| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.59 r_work: 0.3403 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10820 Z= 0.203 Angle : 0.666 9.024 15316 Z= 0.361 Chirality : 0.041 0.238 1813 Planarity : 0.007 0.137 1402 Dihedral : 23.526 176.778 3291 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Rotamer: Outliers : 5.60 % Allowed : 17.60 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.46 (0.27), residues: 885 helix: -0.16 (0.19), residues: 659 sheet: -3.62 (0.81), residues: 28 loop : -3.01 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 111 TYR 0.023 0.003 TYR D 26 PHE 0.027 0.002 PHE A 231 TRP 0.012 0.001 TRP A 15 HIS 0.010 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (10820) covalent geometry : angle 0.66640 / 0.36 (15316) hydrogen bonds : bond 0.06739 / 4.54 ( 607) hydrogen bonds : angle 4.84956 / 3.39 ( 1628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4864 (p90) REVERT: A 82 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8406 (ptmt) REVERT: A 164 THR cc_start: 0.8553 (m) cc_final: 0.8352 (m) REVERT: A 184 LEU cc_start: 0.8828 (tp) cc_final: 0.8455 (tp) REVERT: B 90 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7078 (mttp) REVERT: C 14 MET cc_start: 0.7851 (mtt) cc_final: 0.7538 (mtt) REVERT: D 37 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7862 (ttmm) REVERT: D 89 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: D 98 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: D 108 GLU cc_start: 0.7865 (tp30) cc_final: 0.7379 (tp30) REVERT: D 111 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7595 (mtm180) REVERT: E 14 MET cc_start: 0.6651 (tpp) cc_final: 0.6209 (tpp) REVERT: E 26 TYR cc_start: 0.8141 (t80) cc_final: 0.7391 (t80) REVERT: E 54 GLU cc_start: 0.7887 (tp30) cc_final: 0.7667 (tp30) REVERT: E 98 GLN cc_start: 0.7605 (mt0) cc_final: 0.7222 (mt0) REVERT: F 14 MET cc_start: 0.6636 (mmt) cc_final: 0.5956 (tmm) REVERT: F 19 ARG cc_start: 0.6654 (mmm160) cc_final: 0.5999 (mmm160) outliers start: 42 outliers final: 23 residues processed: 222 average time/residue: 0.1027 time to fit residues: 30.3983 Evaluate side-chains 199 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 32 GLN C 13 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119551 restraints weight = 15930.737| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.63 r_work: 0.3419 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10820 Z= 0.178 Angle : 0.623 9.094 15316 Z= 0.340 Chirality : 0.040 0.238 1813 Planarity : 0.006 0.130 1402 Dihedral : 23.233 177.530 3285 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.88 % Favored : 93.45 % Rotamer: Outliers : 4.40 % Allowed : 17.73 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.08 (0.28), residues: 885 helix: 0.09 (0.19), residues: 659 sheet: -2.93 (0.88), residues: 28 loop : -2.90 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.031 0.002 TYR C 69 PHE 0.042 0.002 PHE B 80 TRP 0.009 0.001 TRP D 116 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (10820) covalent geometry : angle 0.62269 / 0.34 (15316) hydrogen bonds : bond 0.06347 / 4.26 ( 607) hydrogen bonds : angle 4.64689 / 3.26 ( 1628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8509 (m) cc_final: 0.8022 (p) REVERT: A 184 LEU cc_start: 0.8759 (tp) cc_final: 0.8480 (tp) REVERT: B 90 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7066 (mttp) REVERT: C 67 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8424 (mmtp) REVERT: D 18 GLU cc_start: 0.7898 (tp30) cc_final: 0.7612 (mm-30) REVERT: D 19 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7887 (mpt180) REVERT: D 37 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7835 (ttmm) REVERT: D 108 GLU cc_start: 0.7804 (tp30) cc_final: 0.7405 (tp30) REVERT: D 111 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7558 (mtm110) REVERT: E 54 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: F 14 MET cc_start: 0.6493 (mmt) cc_final: 0.5986 (tmm) outliers start: 33 outliers final: 24 residues processed: 211 average time/residue: 0.1104 time to fit residues: 31.2537 Evaluate side-chains 196 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122617 restraints weight = 15901.612| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.67 r_work: 0.3446 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10820 Z= 0.148 Angle : 0.608 10.073 15316 Z= 0.330 Chirality : 0.039 0.247 1813 Planarity : 0.006 0.126 1402 Dihedral : 22.980 177.638 3285 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.55 % Favored : 92.88 % Rotamer: Outliers : 4.40 % Allowed : 19.47 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 885 helix: 0.26 (0.19), residues: 662 sheet: -2.03 (0.96), residues: 26 loop : -2.78 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.034 0.002 TYR C 69 PHE 0.037 0.002 PHE B 80 TRP 0.010 0.001 TRP D 116 HIS 0.007 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (10820) covalent geometry : angle 0.60752 / 0.33 (15316) hydrogen bonds : bond 0.06078 / 4.14 ( 607) hydrogen bonds : angle 4.49977 / 3.17 ( 1628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8505 (m) cc_final: 0.7984 (p) REVERT: B 1 MET cc_start: 0.8513 (ppp) cc_final: 0.7902 (ppp) REVERT: B 90 LYS cc_start: 0.7559 (ttpp) cc_final: 0.7055 (mttp) REVERT: C 67 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8402 (mmtm) REVERT: C 89 GLN cc_start: 0.7106 (tt0) cc_final: 0.6764 (tm-30) REVERT: D 18 GLU cc_start: 0.7712 (tp30) cc_final: 0.7239 (mm-30) REVERT: D 19 ARG cc_start: 0.8070 (mpt180) cc_final: 0.7821 (mpt180) REVERT: D 22 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8278 (mtt-85) REVERT: D 98 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6988 (mt0) REVERT: D 108 GLU cc_start: 0.7878 (tp30) cc_final: 0.7415 (tp30) REVERT: D 111 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7704 (mtm110) REVERT: E 54 GLU cc_start: 0.8000 (tp30) cc_final: 0.7777 (tp30) REVERT: F 14 MET cc_start: 0.6408 (mmt) cc_final: 0.6121 (tmm) REVERT: F 43 GLU cc_start: 0.7736 (tt0) cc_final: 0.7170 (mt-10) REVERT: F 113 LEU cc_start: 0.8564 (tp) cc_final: 0.8181 (tp) outliers start: 33 outliers final: 21 residues processed: 207 average time/residue: 0.1207 time to fit residues: 33.8676 Evaluate side-chains 194 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS B 32 GLN B 92 HIS C 13 GLN C 121 ASN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120188 restraints weight = 16170.096| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.72 r_work: 0.3439 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10820 Z= 0.173 Angle : 0.609 8.113 15316 Z= 0.329 Chirality : 0.039 0.244 1813 Planarity : 0.006 0.124 1402 Dihedral : 22.793 177.690 3284 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.87 % Allowed : 21.87 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 885 helix: 0.35 (0.19), residues: 661 sheet: -1.98 (0.97), residues: 28 loop : -2.74 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 79 TYR 0.030 0.002 TYR F 20 PHE 0.037 0.002 PHE B 80 TRP 0.009 0.001 TRP D 116 HIS 0.012 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10820) covalent geometry : angle 0.60927 / 0.33 (15316) hydrogen bonds : bond 0.06048 / 4.12 ( 607) hydrogen bonds : angle 4.45149 / 3.13 ( 1628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8502 (m) cc_final: 0.8003 (p) REVERT: A 184 LEU cc_start: 0.8907 (tp) cc_final: 0.8499 (tp) REVERT: B 1 MET cc_start: 0.8469 (ppp) cc_final: 0.7771 (ppp) REVERT: B 90 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7056 (mttp) REVERT: C 67 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8472 (mmtp) REVERT: D 18 GLU cc_start: 0.7708 (tp30) cc_final: 0.7238 (mm-30) REVERT: D 19 ARG cc_start: 0.7995 (mpt180) cc_final: 0.7677 (mpt180) REVERT: D 22 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8234 (mtt-85) REVERT: D 108 GLU cc_start: 0.7845 (tp30) cc_final: 0.7542 (tp30) REVERT: E 54 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: F 14 MET cc_start: 0.6323 (mmt) cc_final: 0.5984 (tmm) REVERT: F 113 LEU cc_start: 0.8565 (tp) cc_final: 0.8206 (tp) outliers start: 29 outliers final: 24 residues processed: 197 average time/residue: 0.1208 time to fit residues: 32.0543 Evaluate side-chains 192 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.152929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119295 restraints weight = 15979.884| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.71 r_work: 0.3420 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10820 Z= 0.181 Angle : 0.616 9.673 15316 Z= 0.331 Chirality : 0.039 0.244 1813 Planarity : 0.007 0.124 1402 Dihedral : 22.695 177.655 3284 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Rotamer: Outliers : 4.13 % Allowed : 22.40 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.28), residues: 885 helix: 0.46 (0.19), residues: 662 sheet: -1.97 (0.98), residues: 28 loop : -2.66 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 83 TYR 0.023 0.002 TYR D 69 PHE 0.033 0.002 PHE B 80 TRP 0.009 0.001 TRP D 116 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10820) covalent geometry : angle 0.61576 / 0.33 (15316) hydrogen bonds : bond 0.06077 / 4.16 ( 607) hydrogen bonds : angle 4.48800 / 3.17 ( 1628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8735 (m-40) cc_final: 0.8313 (m-40) REVERT: A 109 CYS cc_start: 0.8386 (m) cc_final: 0.7978 (p) REVERT: A 184 LEU cc_start: 0.8916 (tp) cc_final: 0.8515 (tp) REVERT: B 1 MET cc_start: 0.8535 (ppp) cc_final: 0.7924 (ppp) REVERT: B 90 LYS cc_start: 0.7538 (ttpp) cc_final: 0.7045 (mttp) REVERT: C 67 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8538 (mmtm) REVERT: D 18 GLU cc_start: 0.7525 (tp30) cc_final: 0.7178 (mm-30) REVERT: D 22 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8222 (mtt-85) REVERT: D 37 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7878 (ttmm) REVERT: D 52 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: D 98 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6965 (mt0) REVERT: D 108 GLU cc_start: 0.7966 (tp30) cc_final: 0.7145 (tp30) REVERT: D 111 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7528 (mtm180) REVERT: E 54 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: F 14 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.6029 (tmm) REVERT: F 113 LEU cc_start: 0.8512 (tp) cc_final: 0.8188 (tp) outliers start: 31 outliers final: 22 residues processed: 197 average time/residue: 0.1246 time to fit residues: 32.8582 Evaluate side-chains 197 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.151869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118627 restraints weight = 16208.293| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.60 r_work: 0.3414 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10820 Z= 0.217 Angle : 0.641 9.455 15316 Z= 0.342 Chirality : 0.040 0.240 1813 Planarity : 0.006 0.125 1402 Dihedral : 22.628 177.735 3284 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.55 % Favored : 92.88 % Rotamer: Outliers : 4.67 % Allowed : 21.73 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 885 helix: 0.42 (0.19), residues: 666 sheet: -1.91 (1.01), residues: 28 loop : -2.64 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.024 0.002 TYR D 69 PHE 0.032 0.002 PHE B 80 TRP 0.007 0.001 TRP D 116 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (10820) covalent geometry : angle 0.64087 / 0.34 (15316) hydrogen bonds : bond 0.06234 / 4.26 ( 607) hydrogen bonds : angle 4.52521 / 3.18 ( 1628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8749 (m-40) cc_final: 0.8336 (m-40) REVERT: A 184 LEU cc_start: 0.8937 (tp) cc_final: 0.8511 (tp) REVERT: B 1 MET cc_start: 0.8554 (ppp) cc_final: 0.8025 (ppp) REVERT: B 90 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7097 (mttp) REVERT: C 67 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8548 (mmtm) REVERT: D 18 GLU cc_start: 0.7524 (tp30) cc_final: 0.7222 (mm-30) REVERT: D 22 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8277 (mtt-85) REVERT: D 37 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7912 (ttmm) REVERT: D 52 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: D 92 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.5214 (m90) REVERT: D 98 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: D 108 GLU cc_start: 0.7951 (tp30) cc_final: 0.7561 (tp30) REVERT: E 54 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: F 14 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6013 (tmm) outliers start: 35 outliers final: 27 residues processed: 198 average time/residue: 0.1268 time to fit residues: 33.5235 Evaluate side-chains 203 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 92 HIS C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120127 restraints weight = 16034.391| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.60 r_work: 0.3429 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10820 Z= 0.188 Angle : 0.632 9.236 15316 Z= 0.337 Chirality : 0.040 0.241 1813 Planarity : 0.006 0.125 1402 Dihedral : 22.583 177.500 3284 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 4.53 % Allowed : 22.40 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.28), residues: 885 helix: 0.46 (0.19), residues: 664 sheet: -1.90 (1.01), residues: 28 loop : -2.65 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.024 0.002 TYR C 69 PHE 0.034 0.002 PHE B 80 TRP 0.007 0.001 TRP A 266 HIS 0.018 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10820) covalent geometry : angle 0.63160 / 0.34 (15316) hydrogen bonds : bond 0.06193 / 4.24 ( 607) hydrogen bonds : angle 4.50639 / 3.17 ( 1628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8739 (m-40) cc_final: 0.8319 (m-40) REVERT: A 184 LEU cc_start: 0.8911 (tp) cc_final: 0.8494 (tp) REVERT: B 1 MET cc_start: 0.8556 (ppp) cc_final: 0.7981 (ppp) REVERT: C 67 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8535 (mmtm) REVERT: D 37 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7878 (ttmm) REVERT: D 69 TYR cc_start: 0.8328 (m-80) cc_final: 0.8123 (m-80) REVERT: D 92 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.5240 (m90) REVERT: D 98 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7000 (mt0) REVERT: D 108 GLU cc_start: 0.7822 (tp30) cc_final: 0.7468 (tp30) REVERT: E 54 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: F 14 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6003 (tmm) outliers start: 34 outliers final: 25 residues processed: 196 average time/residue: 0.1231 time to fit residues: 32.5275 Evaluate side-chains 202 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.154946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122058 restraints weight = 16020.743| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.67 r_work: 0.3463 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10820 Z= 0.150 Angle : 0.648 25.263 15316 Z= 0.333 Chirality : 0.038 0.243 1813 Planarity : 0.008 0.199 1402 Dihedral : 22.486 176.946 3280 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 3.87 % Allowed : 22.40 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.28), residues: 885 helix: 0.55 (0.19), residues: 664 sheet: -1.79 (1.03), residues: 28 loop : -2.56 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 19 TYR 0.025 0.002 TYR C 69 PHE 0.037 0.002 PHE B 80 TRP 0.009 0.001 TRP A 266 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10820) covalent geometry : angle 0.64808 / 0.33 (15316) hydrogen bonds : bond 0.06022 / 4.17 ( 607) hydrogen bonds : angle 4.45774 / 3.15 ( 1628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8735 (m-40) cc_final: 0.8320 (m-40) REVERT: A 184 LEU cc_start: 0.8869 (tp) cc_final: 0.8488 (tp) REVERT: B 1 MET cc_start: 0.8507 (ppp) cc_final: 0.7851 (ppp) REVERT: C 67 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8512 (mmtm) REVERT: C 89 GLN cc_start: 0.6968 (tt0) cc_final: 0.6668 (tm-30) REVERT: D 37 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7763 (ttmm) REVERT: D 92 HIS cc_start: 0.6357 (OUTLIER) cc_final: 0.5077 (m90) REVERT: D 108 GLU cc_start: 0.7907 (tp30) cc_final: 0.7217 (tp30) REVERT: E 54 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7622 (tp30) outliers start: 29 outliers final: 23 residues processed: 200 average time/residue: 0.1259 time to fit residues: 33.4927 Evaluate side-chains 201 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121117 restraints weight = 16172.871| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.69 r_work: 0.3456 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10820 Z= 0.170 Angle : 0.666 21.091 15316 Z= 0.343 Chirality : 0.039 0.238 1813 Planarity : 0.007 0.183 1402 Dihedral : 22.424 177.152 3280 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.44 % Favored : 93.11 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.28), residues: 885 helix: 0.56 (0.19), residues: 661 sheet: -1.72 (1.06), residues: 28 loop : -2.53 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 83 TYR 0.023 0.002 TYR C 69 PHE 0.034 0.002 PHE B 80 TRP 0.010 0.001 TRP C 81 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10820) covalent geometry : angle 0.66577 / 0.34 (15316) hydrogen bonds : bond 0.06100 / 4.21 ( 607) hydrogen bonds : angle 4.46740 / 3.15 ( 1628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.98 seconds wall clock time: 41 minutes 45.79 seconds (2505.79 seconds total)