Starting phenix.real_space_refine on Thu Jul 2 20:19:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uba_42080/07_2026/8uba_42080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uba_42080/07_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_42080/07_2026/8uba_42080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uba_42080/07_2026/8uba_42080.map" model { file = "/net/cci-nas-00/data/ceres_data/8uba_42080/07_2026/8uba_42080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uba_42080/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.88, per 1000 atoms: 0.18 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: 0.81 Conformation dependent library (CDL) restraints added in 201.0 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: 1.09 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: 1.63 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: 1.20 - 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: 14019 2.11 - 4.21: 1135 4.21 - 6.32: 130 6.32 - 8.42: 25 8.42 - 10.53: 7 Bond angle restraints: 15316 Sorted by residual: 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 67 " pdb=" O3' U I 67 " pdb=" P C I 68 " ideal model delta sigma weight residual 120.20 110.57 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 120.20 111.20 9.00 1.50e+00 4.44e-01 3.60e+01 angle pdb=" C3' U I 120 " pdb=" O3' U I 120 " pdb=" P G I 121 " ideal model delta sigma weight residual 120.20 111.70 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" C3' U I 7 " pdb=" O3' U I 7 " pdb=" P C I 8 " ideal model delta sigma weight residual 120.20 112.11 8.09 1.50e+00 4.44e-01 2.91e+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: 1589 0.137 - 0.273: 208 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: 1.890 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- 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= 0.661 Angle : 1.251 10.528 15316 Z= 0.824 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 0.01082 / 0.66 (10820) covalent geometry : angle 1.25100 / 0.82 (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 : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7261 (ptp-170) REVERT: A 16 GLU cc_start: 0.8875 (mp0) cc_final: 0.8266 (tm-30) REVERT: A 24 LYS cc_start: 0.8314 (mttp) cc_final: 0.7958 (mtmt) REVERT: A 31 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8025 (mtm110) REVERT: A 68 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7815 (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: 0.8547 (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: 0.7259 (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: 0.8051 (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: 0.7520 (ptmt) REVERT: D 44 MET cc_start: 0.8500 (mtp) cc_final: 0.8287 (mtt) REVERT: D 69 TYR cc_start: 0.8095 (m-80) cc_final: 0.7879 (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: 0.5837 (tpp) REVERT: E 64 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7716 (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: 0.7902 (mmm160) REVERT: F 26 TYR cc_start: 0.8473 (t80) cc_final: 0.8179 (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: 0.7995 (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: 0.1443 time to fit residues: 51.6167 Evaluate side-chains 210 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 9.9990 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: 6.9990 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 = 0.4023 r_free = 0.4023 target = 0.152630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118323 restraints weight = 15726.752| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.79 r_work: 0.3408 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10820 Z= 0.222 Angle : 0.729 13.653 15316 Z= 0.397 Chirality : 0.043 0.238 1813 Planarity : 0.008 0.161 1402 Dihedral : 24.005 176.164 3315 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.33 % Favored : 92.77 % Rotamer: Outliers : 5.73 % Allowed : 16.40 % 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: -2.17 (0.26), residues: 885 helix: -0.68 (0.18), residues: 662 sheet: -4.04 (0.72), residues: 26 loop : -3.27 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.024 0.003 TYR D 26 PHE 0.022 0.003 PHE A 231 TRP 0.013 0.002 TRP C 81 HIS 0.008 0.002 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (10820) covalent geometry : angle 0.72909 / 0.40 (15316) hydrogen bonds : bond 0.07695 / 5.04 ( 607) hydrogen bonds : angle 5.18743 / 3.62 ( 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 248 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6876 (mpt-90) REVERT: A 68 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 161 CYS cc_start: 0.8408 (t) cc_final: 0.8152 (t) REVERT: A 164 THR cc_start: 0.8402 (m) cc_final: 0.8153 (m) REVERT: A 184 LEU cc_start: 0.8749 (tp) cc_final: 0.8393 (tp) REVERT: B 90 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7099 (mttp) REVERT: D 89 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: D 108 GLU cc_start: 0.7756 (tp30) cc_final: 0.7092 (tp30) REVERT: E 14 MET cc_start: 0.6747 (tpp) cc_final: 0.6316 (tpp) REVERT: E 54 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: F 14 MET cc_start: 0.6603 (mmt) cc_final: 0.6028 (tmm) REVERT: F 19 ARG cc_start: 0.7459 (mmm160) cc_final: 0.6680 (mmm160) REVERT: F 43 GLU cc_start: 0.8127 (tt0) cc_final: 0.7391 (mt-10) outliers start: 43 outliers final: 16 residues processed: 233 average time/residue: 0.1223 time to fit residues: 38.2699 Evaluate side-chains 198 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 216 ASP 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: 2.9990 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120378 restraints weight = 15827.051| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.68 r_work: 0.3408 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10820 Z= 0.186 Angle : 0.652 8.851 15316 Z= 0.357 Chirality : 0.042 0.242 1813 Planarity : 0.007 0.136 1402 Dihedral : 23.689 176.119 3291 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.12 % Favored : 92.32 % Rotamer: Outliers : 5.73 % Allowed : 17.47 % 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: -1.44 (0.27), residues: 885 helix: -0.15 (0.19), residues: 660 sheet: -3.21 (0.91), residues: 26 loop : -3.12 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 111 TYR 0.028 0.002 TYR C 69 PHE 0.026 0.002 PHE A 231 TRP 0.012 0.001 TRP A 15 HIS 0.010 0.002 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (10820) covalent geometry : angle 0.65228 / 0.36 (15316) hydrogen bonds : bond 0.06521 / 4.41 ( 607) hydrogen bonds : angle 4.83292 / 3.40 ( 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 239 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.4861 (p90) REVERT: A 82 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8362 (ptmt) REVERT: A 128 ARG cc_start: 0.8045 (ptp-170) cc_final: 0.7819 (ptp-170) REVERT: A 164 THR cc_start: 0.8519 (m) cc_final: 0.8297 (m) REVERT: A 184 LEU cc_start: 0.8770 (tp) cc_final: 0.8444 (tp) REVERT: B 90 LYS cc_start: 0.7547 (ttpp) cc_final: 0.7074 (mttp) REVERT: C 14 MET cc_start: 0.7837 (mtt) cc_final: 0.7517 (mtt) REVERT: C 89 GLN cc_start: 0.7285 (tt0) cc_final: 0.6924 (tm-30) REVERT: D 65 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8562 (t) REVERT: D 98 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7066 (mt0) REVERT: D 108 GLU cc_start: 0.7878 (tp30) cc_final: 0.6898 (tp30) REVERT: D 111 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7457 (mtm180) REVERT: E 54 GLU cc_start: 0.7909 (tp30) cc_final: 0.7678 (tp30) REVERT: F 14 MET cc_start: 0.6585 (mmt) cc_final: 0.5914 (tmm) outliers start: 43 outliers final: 22 residues processed: 226 average time/residue: 0.1260 time to fit residues: 37.9862 Evaluate side-chains 194 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 65 VAL 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 16 ILE 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 E residue 94 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 63 ASN 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: 0.5980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118861 restraints weight = 15871.275| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.69 r_work: 0.3422 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3635 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= 0.183 Angle : 0.623 9.094 15316 Z= 0.342 Chirality : 0.040 0.216 1813 Planarity : 0.006 0.131 1402 Dihedral : 23.443 177.035 3285 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 4.27 % Allowed : 18.00 % Favored : 77.73 % 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: -1.17 (0.27), residues: 885 helix: 0.07 (0.19), residues: 660 sheet: -2.84 (0.93), residues: 28 loop : -3.13 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.029 0.002 TYR C 69 PHE 0.041 0.002 PHE B 80 TRP 0.007 0.001 TRP A 309 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (10820) covalent geometry : angle 0.62269 / 0.34 (15316) hydrogen bonds : bond 0.06268 / 4.21 ( 607) hydrogen bonds : angle 4.67252 / 3.29 ( 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 217 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6847 (mpt-90) REVERT: A 82 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8340 (ptmt) REVERT: A 164 THR cc_start: 0.8541 (m) cc_final: 0.8337 (m) REVERT: A 184 LEU cc_start: 0.8771 (tp) cc_final: 0.8500 (tp) REVERT: B 90 LYS cc_start: 0.7542 (ttpp) cc_final: 0.7065 (mttp) REVERT: C 67 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8387 (mmtm) REVERT: D 18 GLU cc_start: 0.7902 (tp30) cc_final: 0.7466 (mm-30) REVERT: D 19 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7898 (mpt180) REVERT: D 37 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7807 (ttmm) REVERT: D 108 GLU cc_start: 0.7858 (tp30) cc_final: 0.7450 (tp30) REVERT: D 111 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7579 (mtm110) REVERT: E 54 GLU cc_start: 0.8011 (tp30) cc_final: 0.7776 (tp30) REVERT: F 14 MET cc_start: 0.6421 (mmt) cc_final: 0.6068 (tmm) outliers start: 32 outliers final: 23 residues processed: 204 average time/residue: 0.1237 time to fit residues: 34.2575 Evaluate side-chains 193 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.5980 chunk 97 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 18 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121680 restraints weight = 15884.175| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.64 r_work: 0.3447 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10820 Z= 0.154 Angle : 0.602 8.747 15316 Z= 0.330 Chirality : 0.040 0.200 1813 Planarity : 0.006 0.126 1402 Dihedral : 23.181 177.837 3285 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.77 % Rotamer: Outliers : 4.80 % Allowed : 19.20 % Favored : 76.00 % 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: -0.88 (0.28), residues: 885 helix: 0.25 (0.19), residues: 662 sheet: -2.29 (0.97), residues: 28 loop : -3.02 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 36 TYR 0.024 0.002 TYR C 69 PHE 0.041 0.002 PHE B 80 TRP 0.011 0.001 TRP D 116 HIS 0.006 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10820) covalent geometry : angle 0.60157 / 0.33 (15316) hydrogen bonds : bond 0.05966 / 4.07 ( 607) hydrogen bonds : angle 4.54727 / 3.21 ( 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 224 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8394 (ptmt) REVERT: A 164 THR cc_start: 0.8462 (m) cc_final: 0.8260 (m) REVERT: B 90 LYS cc_start: 0.7543 (ttpp) cc_final: 0.7074 (mttp) REVERT: C 14 MET cc_start: 0.7833 (mtt) cc_final: 0.7497 (mtt) REVERT: C 67 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8443 (mmtm) REVERT: D 18 GLU cc_start: 0.7696 (tp30) cc_final: 0.7249 (mm-30) REVERT: D 19 ARG cc_start: 0.8068 (mpt180) cc_final: 0.7819 (mpt180) REVERT: D 22 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8268 (mtt-85) REVERT: D 108 GLU cc_start: 0.7880 (tp30) cc_final: 0.7405 (tp30) REVERT: D 111 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7651 (mtm110) REVERT: F 14 MET cc_start: 0.6309 (mmt) cc_final: 0.6075 (tmm) REVERT: F 43 GLU cc_start: 0.7771 (tt0) cc_final: 0.7215 (mt-10) REVERT: F 113 LEU cc_start: 0.8584 (tp) cc_final: 0.8328 (tp) outliers start: 36 outliers final: 22 residues processed: 211 average time/residue: 0.1177 time to fit residues: 33.6224 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 82 LYS 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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** B 32 GLN B 92 HIS 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 52 GLN F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.156370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124705 restraints weight = 16162.007| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.53 r_work: 0.3496 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10820 Z= 0.156 Angle : 0.600 8.679 15316 Z= 0.328 Chirality : 0.039 0.230 1813 Planarity : 0.006 0.124 1402 Dihedral : 23.003 177.574 3285 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 4.53 % Allowed : 19.73 % Favored : 75.73 % 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: -0.64 (0.28), residues: 885 helix: 0.36 (0.19), residues: 661 sheet: -1.92 (1.01), residues: 28 loop : -2.72 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.030 0.002 TYR F 20 PHE 0.040 0.002 PHE B 80 TRP 0.010 0.001 TRP D 116 HIS 0.012 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10820) covalent geometry : angle 0.59975 / 0.33 (15316) hydrogen bonds : bond 0.05892 / 4.03 ( 607) hydrogen bonds : angle 4.47428 / 3.16 ( 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 218 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8489 (ptmt) REVERT: A 184 LEU cc_start: 0.8936 (tp) cc_final: 0.8483 (tp) REVERT: B 11 TYR cc_start: 0.7644 (t80) cc_final: 0.7408 (t80) REVERT: B 90 LYS cc_start: 0.7323 (ttpp) cc_final: 0.7054 (mttp) REVERT: C 14 MET cc_start: 0.7806 (mtt) cc_final: 0.7478 (mtt) REVERT: C 67 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8579 (mmtm) REVERT: D 18 GLU cc_start: 0.7497 (tp30) cc_final: 0.7245 (mm-30) REVERT: D 19 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7769 (mpt180) REVERT: D 22 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8259 (mtt-85) REVERT: D 52 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: D 98 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: D 108 GLU cc_start: 0.7655 (tp30) cc_final: 0.6925 (tp30) REVERT: D 111 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7458 (mtm-85) REVERT: E 19 ARG cc_start: 0.7379 (mmm160) cc_final: 0.7078 (mmm160) REVERT: F 113 LEU cc_start: 0.8576 (tp) cc_final: 0.8287 (tp) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 0.1322 time to fit residues: 36.2993 Evaluate side-chains 202 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 82 LYS 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 52 GLN Chi-restraints excluded: chain D residue 66 SER 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 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: 10.0000 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 C 121 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.154629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121404 restraints weight = 16006.941| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.71 r_work: 0.3452 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10820 Z= 0.155 Angle : 0.613 9.463 15316 Z= 0.333 Chirality : 0.040 0.282 1813 Planarity : 0.006 0.124 1402 Dihedral : 22.881 177.583 3285 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.77 % Rotamer: Outliers : 3.73 % Allowed : 21.20 % Favored : 75.07 % 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: -0.56 (0.28), residues: 885 helix: 0.42 (0.19), residues: 666 sheet: -1.71 (1.03), residues: 28 loop : -2.84 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.027 0.002 TYR D 69 PHE 0.038 0.002 PHE B 80 TRP 0.009 0.001 TRP D 116 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (10820) covalent geometry : angle 0.61301 / 0.33 (15316) hydrogen bonds : bond 0.05894 / 4.04 ( 607) hydrogen bonds : angle 4.45745 / 3.15 ( 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 211 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8420 (ptmt) REVERT: A 164 THR cc_start: 0.8408 (m) cc_final: 0.8182 (m) REVERT: A 184 LEU cc_start: 0.8918 (tp) cc_final: 0.8471 (tp) REVERT: B 90 LYS cc_start: 0.7522 (ttpp) cc_final: 0.7065 (mttp) REVERT: C 14 MET cc_start: 0.7758 (mtt) cc_final: 0.7385 (mtt) REVERT: C 67 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8497 (mmtm) REVERT: C 89 GLN cc_start: 0.7030 (tt0) cc_final: 0.6675 (tm-30) REVERT: D 18 GLU cc_start: 0.7541 (tp30) cc_final: 0.7158 (mm-30) REVERT: D 19 ARG cc_start: 0.8073 (mpt180) cc_final: 0.7794 (mpt180) REVERT: D 22 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8253 (mtt-85) REVERT: D 108 GLU cc_start: 0.7812 (tp30) cc_final: 0.6972 (tp30) REVERT: D 111 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7629 (mtm-85) REVERT: E 54 GLU cc_start: 0.7899 (tp30) cc_final: 0.7639 (tp30) REVERT: F 113 LEU cc_start: 0.8554 (tp) cc_final: 0.8190 (tp) outliers start: 28 outliers final: 21 residues processed: 201 average time/residue: 0.1316 time to fit residues: 35.3175 Evaluate side-chains 198 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 82 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.152573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.118842 restraints weight = 16196.213| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.73 r_work: 0.3422 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10820 Z= 0.209 Angle : 0.668 20.446 15316 Z= 0.350 Chirality : 0.041 0.261 1813 Planarity : 0.007 0.183 1402 Dihedral : 22.737 178.142 3285 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.33 % Favored : 93.11 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % 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: -0.53 (0.28), residues: 885 helix: 0.44 (0.19), residues: 667 sheet: -1.71 (1.06), residues: 28 loop : -2.81 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.024 0.002 TYR D 69 PHE 0.039 0.002 PHE B 80 TRP 0.008 0.001 TRP F 116 HIS 0.007 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (10820) covalent geometry : angle 0.66842 / 0.35 (15316) hydrogen bonds : bond 0.06073 / 4.13 ( 607) hydrogen bonds : angle 4.49940 / 3.17 ( 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 206 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8809 (m-40) cc_final: 0.8394 (m-40) REVERT: A 109 CYS cc_start: 0.8516 (m) cc_final: 0.8003 (p) REVERT: A 158 LYS cc_start: 0.7942 (mttp) cc_final: 0.7622 (mmtt) REVERT: A 164 THR cc_start: 0.8502 (m) cc_final: 0.8289 (m) REVERT: A 184 LEU cc_start: 0.8926 (tp) cc_final: 0.8489 (tp) REVERT: C 14 MET cc_start: 0.7764 (mtt) cc_final: 0.7368 (mtt) REVERT: C 67 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8499 (mmtm) REVERT: D 18 GLU cc_start: 0.7529 (tp30) cc_final: 0.7287 (mm-30) REVERT: D 19 ARG cc_start: 0.7983 (mpt180) cc_final: 0.7775 (mpt180) REVERT: D 22 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8178 (mtt-85) REVERT: D 94 MET cc_start: 0.7886 (ttt) cc_final: 0.7643 (ttt) REVERT: D 98 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: D 108 GLU cc_start: 0.7777 (tp30) cc_final: 0.6892 (tp30) REVERT: D 111 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7702 (mtm-85) REVERT: F 14 MET cc_start: 0.6323 (tmm) cc_final: 0.5854 (tpp) REVERT: F 26 TYR cc_start: 0.8649 (t80) cc_final: 0.8332 (t80) outliers start: 30 outliers final: 24 residues processed: 197 average time/residue: 0.1349 time to fit residues: 35.1472 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 : 0.267 ------------------------------------------------------------------------------- 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 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 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 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: 0.0980 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.154693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121105 restraints weight = 16077.839| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.73 r_work: 0.3447 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10820 Z= 0.155 Angle : 0.637 16.733 15316 Z= 0.335 Chirality : 0.039 0.301 1813 Planarity : 0.007 0.166 1402 Dihedral : 22.645 177.300 3285 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 3.60 % Allowed : 22.93 % 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: -0.39 (0.28), residues: 885 helix: 0.54 (0.19), residues: 666 sheet: -1.56 (1.09), residues: 28 loop : -2.75 (0.44), residues: 191 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 0.035 0.002 PHE B 80 TRP 0.009 0.001 TRP A 266 HIS 0.014 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10820) covalent geometry : angle 0.63739 / 0.34 (15316) hydrogen bonds : bond 0.05915 / 4.06 ( 607) hydrogen bonds : angle 4.45158 / 3.14 ( 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 205 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8738 (m-40) cc_final: 0.8361 (m-40) REVERT: A 109 CYS cc_start: 0.8490 (m) cc_final: 0.8015 (p) REVERT: A 158 LYS cc_start: 0.7818 (mttp) cc_final: 0.7570 (mmtt) REVERT: A 164 THR cc_start: 0.8419 (m) cc_final: 0.8179 (m) REVERT: A 184 LEU cc_start: 0.8914 (tp) cc_final: 0.8507 (tp) REVERT: B 22 ARG cc_start: 0.8770 (mtm110) cc_final: 0.8507 (mtm-85) REVERT: C 67 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8502 (mmtm) REVERT: D 18 GLU cc_start: 0.7435 (tp30) cc_final: 0.7184 (mm-30) REVERT: D 19 ARG cc_start: 0.7998 (mpt180) cc_final: 0.7697 (mpt180) REVERT: D 22 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8287 (mtt-85) REVERT: D 98 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: D 108 GLU cc_start: 0.7785 (tp30) cc_final: 0.6962 (tp30) REVERT: D 111 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7728 (mtm-85) REVERT: E 54 GLU cc_start: 0.7697 (tp30) cc_final: 0.7474 (tp30) REVERT: F 14 MET cc_start: 0.6323 (tmm) cc_final: 0.5885 (tpp) outliers start: 27 outliers final: 21 residues processed: 195 average time/residue: 0.1310 time to fit residues: 34.1643 Evaluate side-chains 193 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 111 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125196 restraints weight = 15929.263| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.55 r_work: 0.3496 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10820 Z= 0.155 Angle : 0.636 14.214 15316 Z= 0.336 Chirality : 0.039 0.296 1813 Planarity : 0.007 0.157 1402 Dihedral : 22.517 177.051 3280 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.44 % Favored : 93.11 % Rotamer: Outliers : 3.33 % Allowed : 22.13 % Favored : 74.53 % 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: -0.39 (0.28), residues: 885 helix: 0.53 (0.19), residues: 669 sheet: -1.39 (1.12), residues: 28 loop : -2.80 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.029 0.002 TYR C 69 PHE 0.034 0.002 PHE B 80 TRP 0.008 0.001 TRP A 266 HIS 0.005 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10820) covalent geometry : angle 0.63573 / 0.34 (15316) hydrogen bonds : bond 0.05922 / 4.07 ( 607) hydrogen bonds : angle 4.43704 / 3.14 ( 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 194 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8608 (m-40) cc_final: 0.8239 (m-40) REVERT: A 109 CYS cc_start: 0.8365 (m) cc_final: 0.8039 (p) REVERT: A 184 LEU cc_start: 0.8971 (tp) cc_final: 0.8542 (tp) REVERT: B 22 ARG cc_start: 0.8582 (mtm110) cc_final: 0.8306 (mtm-85) REVERT: B 77 MET cc_start: 0.7677 (tpt) cc_final: 0.7424 (tpt) REVERT: C 67 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8564 (mmtm) REVERT: D 19 ARG cc_start: 0.7994 (mpt180) cc_final: 0.7765 (mpt180) REVERT: D 22 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8273 (mtt-85) REVERT: D 98 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: D 108 GLU cc_start: 0.7680 (tp30) cc_final: 0.6987 (tp30) REVERT: E 96 PRO cc_start: 0.8032 (Cg_exo) cc_final: 0.7777 (Cg_endo) REVERT: F 14 MET cc_start: 0.6742 (tmm) cc_final: 0.6289 (tpp) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.1282 time to fit residues: 31.5736 Evaluate side-chains 191 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121650 restraints weight = 16151.999| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.75 r_work: 0.3458 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10820 Z= 0.165 Angle : 0.647 12.689 15316 Z= 0.343 Chirality : 0.039 0.209 1813 Planarity : 0.007 0.151 1402 Dihedral : 22.474 177.146 3280 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.44 % Favored : 93.11 % Rotamer: Outliers : 3.60 % Allowed : 23.33 % 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: -0.32 (0.28), residues: 885 helix: 0.57 (0.19), residues: 667 sheet: -1.31 (1.13), residues: 28 loop : -2.69 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 31 TYR 0.027 0.002 TYR F 20 PHE 0.033 0.002 PHE B 80 TRP 0.009 0.001 TRP A 266 HIS 0.005 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (10820) covalent geometry : angle 0.64720 / 0.34 (15316) hydrogen bonds : bond 0.05959 / 4.10 ( 607) hydrogen bonds : angle 4.44052 / 3.13 ( 1628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.23 seconds wall clock time: 41 minutes 15.21 seconds (2475.21 seconds total)