Starting phenix.real_space_refine on Sat Aug 23 05:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uba_42080/08_2025/8uba_42080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uba_42080/08_2025/8uba_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_2025/8uba_42080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2025/8uba_42080.map" model { file = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2025/8uba_42080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uba_42080/08_2025/8uba_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-2.0-5787/lib/python3.9/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: 2.22, per 1000 atoms: 0.22 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 206.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.10 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: 1.73 Time building geometry restraints manager: 0.99 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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= 0.630 Angle : 1.251 10.528 15316 Z= 0.755 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 aren 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 covalent geometry : bond 0.01082 (10820) covalent geometry : angle 1.25103 (15316) hydrogen bonds : bond 0.20613 ( 607) hydrogen bonds : angle 8.91615 ( 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 : 0.303 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: 0.1359 time to fit residues: 48.3081 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 : 0.307 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 87 GLN B 32 GLN B 92 HIS C 89 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 121 ASN F 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119211 restraints weight = 15793.096| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.67 r_work: 0.3427 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10820 Z= 0.193 Angle : 0.695 11.180 15316 Z= 0.356 Chirality : 0.040 0.238 1813 Planarity : 0.007 0.152 1402 Dihedral : 23.540 175.246 3315 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.77 % Rotamer: Outliers : 5.20 % Allowed : 16.13 % Favored : 78.67 % 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 aren not related in a simple way. whole: -1.68 (0.26), residues: 885 helix: -0.29 (0.18), residues: 667 sheet: -4.19 (0.70), residues: 28 loop : -3.27 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.019 0.002 TYR D 26 PHE 0.024 0.002 PHE A 231 TRP 0.010 0.001 TRP D 116 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00429 (10820) covalent geometry : angle 0.69507 (15316) hydrogen bonds : bond 0.06090 ( 607) hydrogen bonds : angle 4.79949 ( 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 255 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 69 TYR cc_start: 0.5526 (OUTLIER) cc_final: 0.4933 (p90) REVERT: A 113 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6897 (mttm) REVERT: B 90 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7108 (mttp) REVERT: B 108 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: C 54 GLU cc_start: 0.7981 (tt0) cc_final: 0.7772 (mt-10) REVERT: C 67 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8502 (mmtm) REVERT: C 89 GLN cc_start: 0.7110 (tt0) cc_final: 0.6842 (tm-30) REVERT: D 18 GLU cc_start: 0.7748 (tp30) cc_final: 0.7251 (tp30) REVERT: D 37 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7849 (ttmm) REVERT: D 63 ASN cc_start: 0.7074 (m-40) cc_final: 0.6835 (t0) REVERT: D 65 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8597 (t) REVERT: D 108 GLU cc_start: 0.7749 (tp30) cc_final: 0.7143 (tp30) REVERT: E 14 MET cc_start: 0.6788 (tpp) cc_final: 0.6342 (tpp) REVERT: E 54 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: E 72 ASP cc_start: 0.8485 (t70) cc_final: 0.7909 (t70) REVERT: F 14 MET cc_start: 0.6498 (mmt) cc_final: 0.6072 (tmm) REVERT: F 19 ARG cc_start: 0.7330 (mmm160) cc_final: 0.6503 (mmm160) outliers start: 39 outliers final: 13 residues processed: 244 average time/residue: 0.1193 time to fit residues: 38.3955 Evaluate side-chains 198 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 113 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 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL 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 64 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118943 restraints weight = 16016.453| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.60 r_work: 0.3411 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.005 0.053 10820 Z= 0.224 Angle : 0.681 8.950 15316 Z= 0.346 Chirality : 0.039 0.206 1813 Planarity : 0.006 0.131 1402 Dihedral : 23.087 179.227 3289 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.12 % Favored : 92.32 % Rotamer: Outliers : 5.20 % Allowed : 18.40 % Favored : 76.40 % 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 aren not related in a simple way. whole: -1.05 (0.28), residues: 885 helix: 0.14 (0.19), residues: 662 sheet: -3.74 (0.81), residues: 28 loop : -2.90 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 36 TYR 0.025 0.002 TYR D 26 PHE 0.027 0.002 PHE B 80 TRP 0.009 0.001 TRP A 309 HIS 0.008 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00502 (10820) covalent geometry : angle 0.68077 (15316) hydrogen bonds : bond 0.06002 ( 607) hydrogen bonds : angle 4.60519 ( 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 228 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.5966 (mpt-90) REVERT: A 31 ARG cc_start: 0.8276 (mtm110) cc_final: 0.8025 (ttm110) REVERT: A 69 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.5229 (p90) REVERT: A 109 CYS cc_start: 0.8397 (m) cc_final: 0.8109 (p) REVERT: A 184 LEU cc_start: 0.9016 (tp) cc_final: 0.8580 (tp) REVERT: B 90 LYS cc_start: 0.7467 (ttpp) cc_final: 0.7050 (mttp) REVERT: D 18 GLU cc_start: 0.7533 (tp30) cc_final: 0.7299 (mm-30) REVERT: D 22 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8271 (mtt-85) REVERT: D 52 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: D 92 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6465 (m-70) REVERT: D 108 GLU cc_start: 0.7840 (tp30) cc_final: 0.7205 (tp30) REVERT: F 14 MET cc_start: 0.6622 (mmt) cc_final: 0.6213 (tmm) REVERT: F 19 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6330 (mmm160) REVERT: F 94 MET cc_start: 0.6655 (ttp) cc_final: 0.6455 (ttm) outliers start: 39 outliers final: 19 residues processed: 214 average time/residue: 0.1046 time to fit residues: 30.0289 Evaluate side-chains 206 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 256 ARG Chi-restraints excluded: chain B residue 4 ILE 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 92 HIS Chi-restraints excluded: chain D residue 52 GLN 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 16 ILE Chi-restraints excluded: chain E residue 49 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123037 restraints weight = 16038.252| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.56 r_work: 0.3466 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4651 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= 0.159 Angle : 0.613 7.297 15316 Z= 0.314 Chirality : 0.037 0.205 1813 Planarity : 0.006 0.125 1402 Dihedral : 22.653 176.269 3282 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 4.40 % Allowed : 20.27 % Favored : 75.33 % 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 aren not related in a simple way. whole: -0.60 (0.28), residues: 885 helix: 0.43 (0.19), residues: 666 sheet: -2.99 (0.87), residues: 28 loop : -2.72 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 36 TYR 0.020 0.002 TYR C 69 PHE 0.029 0.002 PHE B 80 TRP 0.008 0.001 TRP D 116 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00353 (10820) covalent geometry : angle 0.61263 (15316) hydrogen bonds : bond 0.05561 ( 607) hydrogen bonds : angle 4.40074 ( 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 230 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7201 (t70) cc_final: 0.6979 (t0) REVERT: A 184 LEU cc_start: 0.8912 (tp) cc_final: 0.8573 (tp) REVERT: A 227 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7795 (mp) REVERT: D 22 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8328 (mtt-85) REVERT: D 108 GLU cc_start: 0.7837 (tp30) cc_final: 0.7174 (tp30) REVERT: E 54 GLU cc_start: 0.7714 (tp30) cc_final: 0.7485 (tp30) REVERT: F 19 ARG cc_start: 0.6729 (mmm160) cc_final: 0.6306 (mmm160) REVERT: F 22 ARG cc_start: 0.7360 (mtm180) cc_final: 0.7103 (mtm180) REVERT: F 37 LYS cc_start: 0.8513 (tttm) cc_final: 0.8308 (tttm) outliers start: 33 outliers final: 21 residues processed: 218 average time/residue: 0.1142 time to fit residues: 32.6867 Evaluate side-chains 204 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 227 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 C residue 66 SER 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 16 ILE Chi-restraints excluded: chain E residue 50 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124128 restraints weight = 16009.158| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.56 r_work: 0.3485 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10820 Z= 0.154 Angle : 0.624 9.474 15316 Z= 0.318 Chirality : 0.037 0.208 1813 Planarity : 0.006 0.122 1402 Dihedral : 22.393 176.595 3276 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 4.80 % Allowed : 20.13 % 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 aren not related in a simple way. whole: -0.35 (0.28), residues: 885 helix: 0.62 (0.20), residues: 665 sheet: -2.51 (0.93), residues: 28 loop : -2.75 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 83 TYR 0.027 0.002 TYR F 20 PHE 0.029 0.002 PHE B 80 TRP 0.007 0.001 TRP A 266 HIS 0.012 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00344 (10820) covalent geometry : angle 0.62392 (15316) hydrogen bonds : bond 0.05496 ( 607) hydrogen bonds : angle 4.29044 ( 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 226 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7090 (t70) cc_final: 0.6871 (t0) REVERT: A 184 LEU cc_start: 0.8927 (tp) cc_final: 0.8635 (tp) REVERT: A 227 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 67 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8385 (mmtp) REVERT: C 69 TYR cc_start: 0.8316 (m-80) cc_final: 0.8086 (m-80) REVERT: D 52 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: D 108 GLU cc_start: 0.7862 (tp30) cc_final: 0.7441 (tp30) REVERT: E 26 TYR cc_start: 0.7958 (t80) cc_final: 0.7257 (t80) REVERT: F 14 MET cc_start: 0.6853 (tmm) cc_final: 0.6500 (tpp) REVERT: F 37 LYS cc_start: 0.8470 (tttm) cc_final: 0.8269 (tttp) outliers start: 36 outliers final: 24 residues processed: 215 average time/residue: 0.1127 time to fit residues: 32.1819 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE 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 48 CYS Chi-restraints excluded: chain C residue 92 HIS 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 95 THR 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 50 LEU Chi-restraints excluded: chain E residue 62 SER 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: 0.8980 chunk 7 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122556 restraints weight = 16325.376| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.76 r_work: 0.3464 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10820 Z= 0.144 Angle : 0.617 9.454 15316 Z= 0.313 Chirality : 0.037 0.209 1813 Planarity : 0.006 0.121 1402 Dihedral : 22.246 176.157 3276 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.33 % Allowed : 21.33 % Favored : 75.33 % 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 aren not related in a simple way. whole: -0.17 (0.28), residues: 885 helix: 0.71 (0.20), residues: 666 sheet: -2.00 (1.02), residues: 28 loop : -2.61 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.017 0.002 TYR C 69 PHE 0.023 0.002 PHE B 80 TRP 0.007 0.001 TRP A 266 HIS 0.010 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00319 (10820) covalent geometry : angle 0.61654 (15316) hydrogen bonds : bond 0.05490 ( 607) hydrogen bonds : angle 4.22742 ( 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 211 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8873 (tp) cc_final: 0.8576 (tp) REVERT: A 227 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7707 (mp) REVERT: C 67 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8319 (mmtp) REVERT: C 69 TYR cc_start: 0.8486 (m-10) cc_final: 0.8175 (m-80) REVERT: D 108 GLU cc_start: 0.7989 (tp30) cc_final: 0.7525 (tp30) REVERT: E 54 GLU cc_start: 0.7810 (tp30) cc_final: 0.7589 (tp30) REVERT: F 14 MET cc_start: 0.6827 (tmm) cc_final: 0.6539 (tpp) REVERT: F 22 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7293 (mtm180) REVERT: F 37 LYS cc_start: 0.8394 (tttm) cc_final: 0.8164 (tttm) outliers start: 25 outliers final: 22 residues processed: 202 average time/residue: 0.1167 time to fit residues: 31.0600 Evaluate side-chains 193 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 92 HIS 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 50 LEU Chi-restraints excluded: chain E residue 62 SER 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: 6.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122803 restraints weight = 16068.873| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.74 r_work: 0.3473 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10820 Z= 0.147 Angle : 0.644 20.305 15316 Z= 0.319 Chirality : 0.037 0.209 1813 Planarity : 0.007 0.179 1402 Dihedral : 22.196 176.143 3276 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.65 % Favored : 93.79 % Rotamer: Outliers : 4.27 % Allowed : 21.47 % 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 aren not related in a simple way. whole: -0.01 (0.28), residues: 885 helix: 0.81 (0.20), residues: 665 sheet: -1.80 (1.07), residues: 28 loop : -2.51 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 19 TYR 0.026 0.002 TYR F 20 PHE 0.022 0.002 PHE B 80 TRP 0.008 0.001 TRP A 309 HIS 0.008 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00323 (10820) covalent geometry : angle 0.64373 (15316) hydrogen bonds : bond 0.05489 ( 607) hydrogen bonds : angle 4.22025 ( 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 213 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8893 (tp) cc_final: 0.8579 (tp) REVERT: A 227 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7722 (mp) REVERT: C 67 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8333 (mmtp) REVERT: C 69 TYR cc_start: 0.8432 (m-10) cc_final: 0.8119 (m-80) REVERT: D 19 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7583 (mmt-90) REVERT: D 52 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: D 108 GLU cc_start: 0.7964 (tp30) cc_final: 0.7424 (tp30) REVERT: E 54 GLU cc_start: 0.7802 (tp30) cc_final: 0.7543 (tp30) REVERT: F 37 LYS cc_start: 0.8420 (tttm) cc_final: 0.8190 (tttm) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 0.1024 time to fit residues: 27.8385 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 40 VAL 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 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119047 restraints weight = 16238.987| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.63 r_work: 0.3410 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10820 Z= 0.218 Angle : 0.683 14.203 15316 Z= 0.343 Chirality : 0.039 0.205 1813 Planarity : 0.007 0.157 1402 Dihedral : 22.214 177.891 3276 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.21 % Favored : 93.22 % Rotamer: Outliers : 4.27 % Allowed : 20.93 % Favored : 74.80 % 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 aren not related in a simple way. whole: -0.18 (0.28), residues: 885 helix: 0.65 (0.19), residues: 667 sheet: -1.86 (1.08), residues: 28 loop : -2.42 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.014 0.002 TYR C 28 PHE 0.026 0.002 PHE B 80 TRP 0.008 0.001 TRP A 15 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00492 (10820) covalent geometry : angle 0.68320 (15316) hydrogen bonds : bond 0.05920 ( 607) hydrogen bonds : angle 4.36247 ( 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 207 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8535 (t0) cc_final: 0.8140 (t0) REVERT: A 184 LEU cc_start: 0.8964 (tp) cc_final: 0.8574 (tp) REVERT: A 227 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7758 (mp) REVERT: C 67 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8288 (mmtp) REVERT: C 69 TYR cc_start: 0.8478 (m-10) cc_final: 0.8224 (m-80) REVERT: D 52 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8540 (tm-30) REVERT: D 108 GLU cc_start: 0.8067 (tp30) cc_final: 0.7719 (tp30) REVERT: E 54 GLU cc_start: 0.8031 (tp30) cc_final: 0.7762 (tp30) REVERT: F 37 LYS cc_start: 0.8514 (tttm) cc_final: 0.8259 (tttm) outliers start: 32 outliers final: 27 residues processed: 196 average time/residue: 0.1108 time to fit residues: 28.6831 Evaluate side-chains 197 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL 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 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 103 GLN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121258 restraints weight = 16358.080| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.96 r_work: 0.3455 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10820 Z= 0.145 Angle : 0.640 11.515 15316 Z= 0.324 Chirality : 0.037 0.201 1813 Planarity : 0.006 0.146 1402 Dihedral : 22.042 176.095 3276 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.54 % Favored : 93.90 % Rotamer: Outliers : 4.13 % Allowed : 21.20 % Favored : 74.67 % 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 aren not related in a simple way. whole: 0.01 (0.28), residues: 885 helix: 0.81 (0.20), residues: 665 sheet: -1.78 (1.09), residues: 28 loop : -2.43 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 19 TYR 0.022 0.002 TYR F 20 PHE 0.021 0.002 PHE B 80 TRP 0.008 0.001 TRP A 266 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00316 (10820) covalent geometry : angle 0.64027 (15316) hydrogen bonds : bond 0.05622 ( 607) hydrogen bonds : angle 4.24744 ( 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 207 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8856 (tp) cc_final: 0.8503 (tp) REVERT: A 227 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7714 (mp) REVERT: C 67 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8276 (mmtp) REVERT: C 69 TYR cc_start: 0.8433 (m-10) cc_final: 0.8190 (m-80) REVERT: C 89 GLN cc_start: 0.6901 (tt0) cc_final: 0.6576 (tm-30) REVERT: D 14 MET cc_start: 0.7738 (tpt) cc_final: 0.6743 (mtm) REVERT: D 52 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: D 108 GLU cc_start: 0.8023 (tp30) cc_final: 0.7569 (tp30) REVERT: E 54 GLU cc_start: 0.7887 (tp30) cc_final: 0.7581 (tp30) REVERT: F 37 LYS cc_start: 0.8277 (tttm) cc_final: 0.8068 (tttm) outliers start: 31 outliers final: 27 residues processed: 197 average time/residue: 0.1036 time to fit residues: 27.2893 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 15 LEU 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 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 103 GLN 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: 0.6980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119181 restraints weight = 16318.713| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.94 r_work: 0.3421 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10820 Z= 0.182 Angle : 0.676 10.535 15316 Z= 0.342 Chirality : 0.039 0.197 1813 Planarity : 0.006 0.142 1402 Dihedral : 22.040 177.038 3276 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.87 % Allowed : 22.00 % Favored : 74.13 % 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 aren not related in a simple way. whole: -0.00 (0.29), residues: 885 helix: 0.76 (0.19), residues: 668 sheet: -1.75 (1.08), residues: 28 loop : -2.33 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.012 0.002 TYR C 69 PHE 0.029 0.002 PHE B 80 TRP 0.008 0.001 TRP F 116 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00408 (10820) covalent geometry : angle 0.67555 (15316) hydrogen bonds : bond 0.05749 ( 607) hydrogen bonds : angle 4.29907 ( 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 198 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8939 (tp) cc_final: 0.8555 (tp) REVERT: A 227 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7677 (mp) REVERT: C 67 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8287 (mmtp) REVERT: C 69 TYR cc_start: 0.8465 (m-10) cc_final: 0.8240 (m-80) REVERT: C 89 GLN cc_start: 0.7015 (tt0) cc_final: 0.6673 (tm-30) REVERT: D 14 MET cc_start: 0.7739 (tpt) cc_final: 0.6987 (ttm) REVERT: D 19 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7801 (tpp80) REVERT: D 37 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7926 (ptmm) REVERT: E 26 TYR cc_start: 0.8000 (t80) cc_final: 0.7709 (t80) REVERT: E 54 GLU cc_start: 0.7944 (tp30) cc_final: 0.7629 (tp30) outliers start: 29 outliers final: 26 residues processed: 189 average time/residue: 0.1040 time to fit residues: 26.3131 Evaluate side-chains 191 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 40 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 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 103 GLN 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: 0.5980 chunk 28 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120200 restraints weight = 16476.729| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.95 r_work: 0.3437 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10820 Z= 0.166 Angle : 0.663 9.792 15316 Z= 0.336 Chirality : 0.038 0.195 1813 Planarity : 0.006 0.139 1402 Dihedral : 22.022 176.680 3276 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 3.60 % Allowed : 22.67 % 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 aren not related in a simple way. whole: 0.05 (0.28), residues: 885 helix: 0.82 (0.19), residues: 664 sheet: -1.61 (1.10), residues: 28 loop : -2.34 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.012 0.002 TYR C 69 PHE 0.025 0.002 PHE B 80 TRP 0.008 0.001 TRP A 266 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00370 (10820) covalent geometry : angle 0.66266 (15316) hydrogen bonds : bond 0.05667 ( 607) hydrogen bonds : angle 4.30358 ( 1628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.79 seconds wall clock time: 36 minutes 9.94 seconds (2169.94 seconds total)