Starting phenix.real_space_refine on Wed Mar 4 22:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.map" model { file = "/net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bge_12179/03_2026/7bge_12179.cif" } resolution = 3.6 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= 0.006 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 465 5.49 5 S 21 5.16 5 C 8882 2.51 5 N 3119 2.21 5 O 4501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16988 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 9920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 9920 Classifications: {'RNA': 465} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 35, 'rna3p_pur': 204, 'rna3p_pyr': 182} Link IDs: {'rna2p': 79, 'rna3p': 385} Chain: "b" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 864 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Chain: "c" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1596 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "g" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1177 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "i" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 987 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "j" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 773 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "m" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 584 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 2 Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 497 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "s" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 2.89, per 1000 atoms: 0.17 Number of scatterers: 16988 At special positions: 0 Unit cell: (116.62, 119, 135.66, 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 21 16.00 P 465 15.00 O 4501 8.00 N 3119 7.00 C 8882 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: 1.42 Conformation dependent library (CDL) restraints added in 456.5 milliseconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.0% alpha, 12.1% beta 133 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'b' and resid 107 through 120 removed outlier: 3.798A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 147 removed outlier: 3.939A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 174 Processing helix chain 'c' and resid 28 through 50 removed outlier: 3.889A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU c 34 " --> pdb=" O SER c 30 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS c 47 " --> pdb=" O ASP c 43 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER c 50 " --> pdb=" O LEU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 75 removed outlier: 3.684A pdb=" N MET c 74 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 75 " --> pdb=" O PRO c 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 75' Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.652A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.521A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.078A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.801A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR g 44 " --> pdb=" O GLN g 40 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER g 45 " --> pdb=" O ARG g 41 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.612A pdb=" N ASN g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.635A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN g 122 " --> pdb=" O ASP g 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 148 Processing helix chain 'i' and resid 52 through 57 removed outlier: 3.506A pdb=" N THR i 57 " --> pdb=" O PRO i 53 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 93 Processing helix chain 'i' and resid 96 through 102 Processing helix chain 'j' and resid 15 through 32 removed outlier: 3.518A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER j 21 " --> pdb=" O VAL j 17 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.945A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 81 Processing helix chain 'm' and resid 106 through 110 Processing helix chain 'n' and resid 4 through 11 removed outlier: 3.603A pdb=" N GLN n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.636A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 22 removed outlier: 3.724A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 161 through 163 removed outlier: 6.020A pdb=" N LEU b 161 " --> pdb=" O VAL b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.853A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL c 54 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA c 66 " --> pdb=" O VAL c 54 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE c 67 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 166 removed outlier: 3.515A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 166 removed outlier: 3.515A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 73 through 74 removed outlier: 3.549A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 11 through 13 removed outlier: 6.144A pdb=" N THR i 31 " --> pdb=" O VAL i 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'j' and resid 6 through 11 removed outlier: 4.677A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 47 through 52 Processing sheet with id=AA9, first strand: chain 's' and resid 31 through 33 removed outlier: 6.711A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR s 33 " --> pdb=" O TYR s 52 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 524 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2413 1.33 - 1.45: 7170 1.45 - 1.57: 7722 1.57 - 1.69: 932 1.69 - 1.81: 37 Bond restraints: 18274 Sorted by residual: bond pdb=" C ARG g 92 " pdb=" N PRO g 93 " ideal model delta sigma weight residual 1.335 1.394 -0.060 1.19e-02 7.06e+03 2.50e+01 bond pdb=" C GLN i 52 " pdb=" N PRO i 53 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.06e-02 8.90e+03 7.62e+00 bond pdb=" CA ARG i 124 " pdb=" CB ARG i 124 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.48e-02 4.57e+03 5.38e+00 bond pdb=" N PRO s 42 " pdb=" CA PRO s 42 " ideal model delta sigma weight residual 1.468 1.485 -0.018 7.90e-03 1.60e+04 5.06e+00 bond pdb=" N1 C a 946 " pdb=" C2 C a 946 " ideal model delta sigma weight residual 1.397 1.442 -0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 18269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 25632 2.87 - 5.74: 1158 5.74 - 8.61: 104 8.61 - 11.47: 25 11.47 - 14.34: 5 Bond angle restraints: 26924 Sorted by residual: angle pdb=" C ALA i 123 " pdb=" N ARG i 124 " pdb=" CA ARG i 124 " ideal model delta sigma weight residual 122.63 133.59 -10.96 1.44e+00 4.82e-01 5.79e+01 angle pdb=" CA ARG i 124 " pdb=" CB ARG i 124 " pdb=" CG ARG i 124 " ideal model delta sigma weight residual 114.10 126.96 -12.86 2.00e+00 2.50e-01 4.13e+01 angle pdb=" C GLY b 99 " pdb=" N LEU b 100 " pdb=" CA LEU b 100 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C3' U a1054 " pdb=" O3' U a1054 " pdb=" P G a1055 " ideal model delta sigma weight residual 120.20 129.45 -9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" C ASN i 33 " pdb=" N ASN i 34 " pdb=" CA ASN i 34 " ideal model delta sigma weight residual 122.08 131.11 -9.03 1.47e+00 4.63e-01 3.77e+01 ... (remaining 26919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 10367 35.70 - 71.40: 1130 71.40 - 107.10: 137 107.10 - 142.80: 1 142.80 - 178.50: 5 Dihedral angle restraints: 11640 sinusoidal: 9113 harmonic: 2527 Sorted by residual: dihedral pdb=" O4' U a1034 " pdb=" C1' U a1034 " pdb=" N1 U a1034 " pdb=" C2 U a1034 " ideal model delta sinusoidal sigma weight residual 200.00 40.55 159.45 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' C a1169 " pdb=" C1' C a1169 " pdb=" N1 C a1169 " pdb=" C2 C a1169 " ideal model delta sinusoidal sigma weight residual 200.00 67.17 132.83 1 1.50e+01 4.44e-03 7.17e+01 dihedral pdb=" O4' U a 970 " pdb=" C1' U a 970 " pdb=" N1 U a 970 " pdb=" C2 U a 970 " ideal model delta sinusoidal sigma weight residual -128.00 50.50 -178.50 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2998 0.092 - 0.183: 342 0.183 - 0.275: 38 0.275 - 0.367: 8 0.367 - 0.458: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C3' U a1054 " pdb=" C4' U a1054 " pdb=" O3' U a1054 " pdb=" C2' U a1054 " both_signs ideal model delta sigma weight residual False -2.48 -2.02 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CB VAL c 172 " pdb=" CA VAL c 172 " pdb=" CG1 VAL c 172 " pdb=" CG2 VAL c 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB ILE c 65 " pdb=" CA ILE c 65 " pdb=" CG1 ILE c 65 " pdb=" CG2 ILE c 65 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 3384 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO j 43 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG c 39 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ARG c 39 " 0.076 2.00e-02 2.50e+03 pdb=" O ARG c 39 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS c 40 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE c 28 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C PHE c 28 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE c 28 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA c 29 " 0.025 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4500 2.82 - 3.34: 12418 3.34 - 3.86: 35251 3.86 - 4.38: 39940 4.38 - 4.90: 55929 Nonbonded interactions: 148038 Sorted by model distance: nonbonded pdb=" O2' U a1332 " pdb=" NE ARG s 78 " model vdw 2.296 3.120 nonbonded pdb=" O2' U a1246 " pdb=" OP1 G a1316 " model vdw 2.339 3.040 nonbonded pdb=" O2' C a1260 " pdb=" O GLY i 72 " model vdw 2.356 3.040 nonbonded pdb=" O2' G a1281 " pdb=" O2' U a1324 " model vdw 2.370 3.040 nonbonded pdb=" O2 C a1126 " pdb=" OG SER n 60 " model vdw 2.371 3.040 ... (remaining 148033 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.006 0.061 18274 Z= 0.338 Angle : 1.329 14.342 26924 Z= 0.653 Chirality : 0.059 0.458 3387 Planarity : 0.009 0.115 1703 Dihedral : 22.858 178.504 10008 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.29 % Favored : 89.59 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % Cbeta Deviations : 0.37 % 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: -5.86 (0.20), residues: 855 helix: -4.56 (0.12), residues: 303 sheet: -2.20 (0.41), residues: 139 loop : -3.99 (0.22), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG j 68 TYR 0.029 0.003 TYR g 107 PHE 0.036 0.004 PHE s 44 TRP 0.049 0.004 TRP c 200 HIS 0.007 0.001 HIS s 69 Details of bonding type rmsd covalent geometry : bond 0.00649 (18274) covalent geometry : angle 1.32928 (26924) hydrogen bonds : bond 0.15328 ( 549) hydrogen bonds : angle 6.78853 ( 1172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 8 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7935 (Cg_exo) REVERT: g 10 ARG cc_start: 0.5093 (pmt170) cc_final: 0.3955 (tmm-80) REVERT: g 91 VAL cc_start: 0.6203 (m) cc_final: 0.5214 (m) REVERT: g 116 MET cc_start: 0.7983 (tpt) cc_final: 0.7739 (tpt) REVERT: s 27 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5483 (mtmt) outliers start: 16 outliers final: 3 residues processed: 273 average time/residue: 0.1715 time to fit residues: 65.1180 Evaluate side-chains 179 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain s residue 27 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 103 ASN c 3 GLN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 ASN c 99 HIS c 125 ASN g 28 ASN i 70 HIS j 67 GLN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 GLN s 47 HIS s 57 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108406 restraints weight = 30966.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110140 restraints weight = 21661.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110482 restraints weight = 13648.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110670 restraints weight = 12593.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110885 restraints weight = 11642.197| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18274 Z= 0.151 Angle : 0.638 7.816 26924 Z= 0.333 Chirality : 0.037 0.240 3387 Planarity : 0.006 0.073 1703 Dihedral : 23.152 178.689 8181 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.93 % Allowed : 19.68 % Favored : 77.39 % 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: -4.25 (0.23), residues: 855 helix: -2.39 (0.23), residues: 315 sheet: -1.91 (0.42), residues: 142 loop : -3.55 (0.25), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG i 102 TYR 0.010 0.001 TYR n 21 PHE 0.015 0.001 PHE s 44 TRP 0.025 0.002 TRP c 200 HIS 0.005 0.001 HIS i 70 Details of bonding type rmsd covalent geometry : bond 0.00310 (18274) covalent geometry : angle 0.63824 (26924) hydrogen bonds : bond 0.06170 ( 549) hydrogen bonds : angle 4.10344 ( 1172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 153 SER cc_start: 0.9042 (m) cc_final: 0.8828 (m) REVERT: g 10 ARG cc_start: 0.5895 (pmt170) cc_final: 0.4913 (pmt-80) REVERT: i 105 LEU cc_start: 0.8973 (mp) cc_final: 0.8761 (mp) REVERT: s 27 LYS cc_start: 0.6048 (mttm) cc_final: 0.5809 (mtmm) REVERT: s 34 TRP cc_start: 0.8502 (m100) cc_final: 0.8048 (m100) outliers start: 22 outliers final: 8 residues processed: 207 average time/residue: 0.1317 time to fit residues: 41.0248 Evaluate side-chains 172 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain i residue 70 HIS Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain n residue 61 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 115 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 151 GLN g 67 ASN j 15 HIS j 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097884 restraints weight = 31601.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100189 restraints weight = 22843.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100265 restraints weight = 13798.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100465 restraints weight = 12560.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100547 restraints weight = 11758.782| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18274 Z= 0.290 Angle : 0.737 11.105 26924 Z= 0.377 Chirality : 0.041 0.267 3387 Planarity : 0.006 0.073 1703 Dihedral : 23.113 178.669 8174 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.58 % Favored : 88.30 % Rotamer: Outliers : 5.05 % Allowed : 18.75 % Favored : 76.20 % 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: -3.34 (0.26), residues: 855 helix: -1.12 (0.28), residues: 305 sheet: -1.87 (0.44), residues: 133 loop : -3.27 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 102 TYR 0.018 0.002 TYR b 104 PHE 0.022 0.002 PHE s 44 TRP 0.035 0.002 TRP c 200 HIS 0.006 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00580 (18274) covalent geometry : angle 0.73673 (26924) hydrogen bonds : bond 0.06878 ( 549) hydrogen bonds : angle 4.12835 ( 1172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.400 Fit side-chains REVERT: b 189 THR cc_start: 0.3331 (OUTLIER) cc_final: 0.3012 (p) REVERT: c 45 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: c 122 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.6570 (mp-120) REVERT: c 151 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8447 (tm130) REVERT: c 200 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7397 (m100) REVERT: g 15 ASP cc_start: 0.8003 (p0) cc_final: 0.7690 (p0) REVERT: g 70 MET cc_start: 0.6791 (tmm) cc_final: 0.6542 (tmm) REVERT: i 47 ILE cc_start: 0.8203 (pt) cc_final: 0.7991 (mp) REVERT: j 27 GLU cc_start: 0.6335 (tm-30) cc_final: 0.6071 (tm-30) REVERT: s 34 TRP cc_start: 0.8641 (m100) cc_final: 0.8243 (m100) REVERT: s 74 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7721 (m-80) outliers start: 38 outliers final: 20 residues processed: 201 average time/residue: 0.1430 time to fit residues: 42.6876 Evaluate side-chains 186 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN c 166 GLN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 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 = 0.3608 r_free = 0.3608 target = 0.121474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100216 restraints weight = 31213.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102386 restraints weight = 21427.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102386 restraints weight = 14242.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102664 restraints weight = 12653.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102722 restraints weight = 11405.852| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18274 Z= 0.218 Angle : 0.661 10.885 26924 Z= 0.339 Chirality : 0.038 0.254 3387 Planarity : 0.005 0.070 1703 Dihedral : 23.102 179.918 8174 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 4.52 % Allowed : 24.07 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.27), residues: 855 helix: -0.51 (0.30), residues: 303 sheet: -1.88 (0.44), residues: 136 loop : -3.07 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG g 96 TYR 0.011 0.001 TYR b 104 PHE 0.023 0.002 PHE s 44 TRP 0.030 0.002 TRP c 200 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd covalent geometry : bond 0.00439 (18274) covalent geometry : angle 0.66106 (26924) hydrogen bonds : bond 0.06134 ( 549) hydrogen bonds : angle 3.89812 ( 1172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 45 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: c 200 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.7250 (m100) REVERT: g 15 ASP cc_start: 0.7920 (p0) cc_final: 0.7623 (p0) REVERT: i 49 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6104 (m-30) REVERT: m 25 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6903 (mp) REVERT: s 34 TRP cc_start: 0.8549 (m100) cc_final: 0.8215 (m100) REVERT: s 74 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7500 (m-80) outliers start: 34 outliers final: 21 residues processed: 188 average time/residue: 0.1380 time to fit residues: 38.5758 Evaluate side-chains 190 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 68 ASN ** s 47 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 = 0.3611 r_free = 0.3611 target = 0.121707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100292 restraints weight = 31293.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101823 restraints weight = 22521.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102280 restraints weight = 14444.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102390 restraints weight = 12370.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102674 restraints weight = 11608.657| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18274 Z= 0.208 Angle : 0.644 10.169 26924 Z= 0.330 Chirality : 0.038 0.251 3387 Planarity : 0.005 0.071 1703 Dihedral : 23.074 179.950 8174 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.98 % Allowed : 23.94 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.28), residues: 855 helix: -0.18 (0.31), residues: 299 sheet: -1.81 (0.45), residues: 138 loop : -2.91 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 102 TYR 0.009 0.001 TYR n 21 PHE 0.019 0.002 PHE s 44 TRP 0.030 0.002 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd covalent geometry : bond 0.00420 (18274) covalent geometry : angle 0.64422 (26924) hydrogen bonds : bond 0.06001 ( 549) hydrogen bonds : angle 3.80971 ( 1172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: b 189 THR cc_start: 0.3434 (OUTLIER) cc_final: 0.3150 (p) REVERT: c 45 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: c 126 ARG cc_start: 0.7889 (ptt180) cc_final: 0.7602 (ptt180) REVERT: c 200 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7204 (m100) REVERT: i 47 ILE cc_start: 0.8375 (pt) cc_final: 0.8167 (mp) REVERT: i 49 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: j 27 GLU cc_start: 0.6394 (tm-30) cc_final: 0.6176 (tm-30) REVERT: j 82 LYS cc_start: 0.7959 (mppt) cc_final: 0.7518 (mtmm) REVERT: s 34 TRP cc_start: 0.8538 (m100) cc_final: 0.8258 (m100) REVERT: s 74 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7536 (m-80) outliers start: 45 outliers final: 26 residues processed: 205 average time/residue: 0.1247 time to fit residues: 38.6569 Evaluate side-chains 197 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 70 MET Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN c 122 GLN c 151 GLN g 67 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098293 restraints weight = 31357.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098548 restraints weight = 22044.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101438 restraints weight = 18135.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101316 restraints weight = 11250.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101409 restraints weight = 10168.538| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18274 Z= 0.266 Angle : 0.693 9.986 26924 Z= 0.354 Chirality : 0.040 0.252 3387 Planarity : 0.005 0.072 1703 Dihedral : 23.045 178.701 8174 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 6.52 % Allowed : 25.13 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.29), residues: 855 helix: -0.23 (0.31), residues: 302 sheet: -1.78 (0.46), residues: 137 loop : -2.83 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 102 TYR 0.019 0.001 TYR c 23 PHE 0.019 0.002 PHE s 44 TRP 0.032 0.002 TRP c 200 HIS 0.005 0.001 HIS s 14 Details of bonding type rmsd covalent geometry : bond 0.00534 (18274) covalent geometry : angle 0.69274 (26924) hydrogen bonds : bond 0.06403 ( 549) hydrogen bonds : angle 3.97840 ( 1172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3856 (OUTLIER) cc_final: 0.3626 (p) REVERT: c 122 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.6909 (mp-120) REVERT: c 126 ARG cc_start: 0.7863 (ptt180) cc_final: 0.7587 (ptt180) REVERT: c 151 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: c 200 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7283 (m100) REVERT: g 64 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: i 39 GLU cc_start: 0.6267 (tt0) cc_final: 0.5945 (tt0) REVERT: i 115 ARG cc_start: 0.6900 (ptp-170) cc_final: 0.6645 (ptp90) REVERT: j 82 LYS cc_start: 0.7913 (mppt) cc_final: 0.7693 (mtmm) REVERT: m 25 ILE cc_start: 0.7535 (mp) cc_final: 0.7300 (mp) REVERT: s 34 TRP cc_start: 0.8568 (m100) cc_final: 0.8225 (m100) REVERT: s 74 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7722 (m-80) outliers start: 49 outliers final: 34 residues processed: 209 average time/residue: 0.1319 time to fit residues: 41.5448 Evaluate side-chains 215 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0000 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 151 GLN g 67 ASN g 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103569 restraints weight = 30921.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105787 restraints weight = 21828.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105748 restraints weight = 14427.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105849 restraints weight = 12595.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106372 restraints weight = 11272.591| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18274 Z= 0.148 Angle : 0.606 10.562 26924 Z= 0.311 Chirality : 0.036 0.249 3387 Planarity : 0.005 0.068 1703 Dihedral : 23.048 179.364 8174 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.85 % Allowed : 26.73 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.29), residues: 855 helix: -0.09 (0.31), residues: 313 sheet: -1.72 (0.46), residues: 138 loop : -2.97 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG i 102 TYR 0.008 0.001 TYR b 104 PHE 0.017 0.001 PHE s 44 TRP 0.025 0.002 TRP c 200 HIS 0.008 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00297 (18274) covalent geometry : angle 0.60617 (26924) hydrogen bonds : bond 0.05561 ( 549) hydrogen bonds : angle 3.69890 ( 1172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: b 189 THR cc_start: 0.3402 (OUTLIER) cc_final: 0.3171 (p) REVERT: c 122 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8331 (mp10) REVERT: c 200 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7099 (m100) REVERT: i 37 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8214 (t) REVERT: i 39 GLU cc_start: 0.5981 (tt0) cc_final: 0.5717 (tt0) REVERT: s 34 TRP cc_start: 0.8470 (m100) cc_final: 0.8110 (m100) outliers start: 44 outliers final: 25 residues processed: 215 average time/residue: 0.1312 time to fit residues: 42.3449 Evaluate side-chains 207 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 67 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103094 restraints weight = 31346.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105441 restraints weight = 21154.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105683 restraints weight = 13836.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105801 restraints weight = 12240.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105875 restraints weight = 10432.894| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18274 Z= 0.166 Angle : 0.625 17.032 26924 Z= 0.317 Chirality : 0.037 0.261 3387 Planarity : 0.005 0.070 1703 Dihedral : 22.986 178.920 8174 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.35 % Favored : 88.54 % Rotamer: Outliers : 4.79 % Allowed : 27.66 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.29), residues: 855 helix: -0.09 (0.31), residues: 313 sheet: -1.50 (0.49), residues: 121 loop : -2.79 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG i 102 TYR 0.013 0.001 TYR c 23 PHE 0.020 0.001 PHE s 44 TRP 0.026 0.001 TRP c 200 HIS 0.008 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00340 (18274) covalent geometry : angle 0.62486 (26924) hydrogen bonds : bond 0.05555 ( 549) hydrogen bonds : angle 3.68994 ( 1172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3517 (OUTLIER) cc_final: 0.3304 (p) REVERT: c 151 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: c 200 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.7114 (m100) REVERT: i 37 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (t) REVERT: i 39 GLU cc_start: 0.5981 (tt0) cc_final: 0.5694 (tt0) REVERT: i 63 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: m 109 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8261 (mmm-85) REVERT: s 34 TRP cc_start: 0.8534 (m100) cc_final: 0.8117 (m100) REVERT: s 74 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7554 (m-80) outliers start: 36 outliers final: 27 residues processed: 199 average time/residue: 0.1372 time to fit residues: 40.3802 Evaluate side-chains 208 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 63 TYR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 67 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 70 HIS ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101603 restraints weight = 31104.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103211 restraints weight = 21349.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103609 restraints weight = 14111.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103704 restraints weight = 12134.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103936 restraints weight = 11324.166| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18274 Z= 0.198 Angle : 0.645 12.582 26924 Z= 0.328 Chirality : 0.038 0.271 3387 Planarity : 0.005 0.071 1703 Dihedral : 22.962 178.918 8174 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.99 % Favored : 88.89 % Rotamer: Outliers : 4.92 % Allowed : 26.99 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.29), residues: 855 helix: -0.21 (0.31), residues: 317 sheet: -1.31 (0.48), residues: 127 loop : -2.77 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 87 TYR 0.013 0.001 TYR i 96 PHE 0.018 0.001 PHE s 44 TRP 0.028 0.002 TRP c 200 HIS 0.008 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00402 (18274) covalent geometry : angle 0.64510 (26924) hydrogen bonds : bond 0.05773 ( 549) hydrogen bonds : angle 3.76625 ( 1172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: c 101 ASN cc_start: 0.7899 (t0) cc_final: 0.7683 (t0) REVERT: c 109 ASP cc_start: 0.7742 (p0) cc_final: 0.7443 (p0) REVERT: c 126 ARG cc_start: 0.7793 (ptt180) cc_final: 0.7519 (ptt180) REVERT: c 151 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8639 (tm-30) REVERT: c 200 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.7197 (m100) REVERT: i 37 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (t) REVERT: i 39 GLU cc_start: 0.6051 (tt0) cc_final: 0.5762 (tt0) REVERT: i 63 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: m 95 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5472 (tp) REVERT: m 109 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8315 (mmm-85) REVERT: s 34 TRP cc_start: 0.8552 (m100) cc_final: 0.8251 (m100) REVERT: s 74 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7556 (m-80) outliers start: 37 outliers final: 28 residues processed: 197 average time/residue: 0.1323 time to fit residues: 39.0043 Evaluate side-chains 209 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 63 TYR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 67 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102838 restraints weight = 30940.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104886 restraints weight = 21224.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104973 restraints weight = 14381.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105216 restraints weight = 12560.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105282 restraints weight = 11235.868| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18274 Z= 0.175 Angle : 0.627 14.818 26924 Z= 0.318 Chirality : 0.037 0.274 3387 Planarity : 0.005 0.070 1703 Dihedral : 22.951 179.186 8174 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.11 % Favored : 88.77 % Rotamer: Outliers : 4.79 % Allowed : 26.99 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.29), residues: 855 helix: -0.02 (0.31), residues: 309 sheet: -1.20 (0.48), residues: 126 loop : -2.70 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG i 102 TYR 0.010 0.001 TYR i 96 PHE 0.019 0.001 PHE s 44 TRP 0.027 0.001 TRP c 200 HIS 0.009 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00355 (18274) covalent geometry : angle 0.62706 (26924) hydrogen bonds : bond 0.05618 ( 549) hydrogen bonds : angle 3.71210 ( 1172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: c 126 ARG cc_start: 0.7804 (ptt180) cc_final: 0.7545 (ptt180) REVERT: c 151 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: c 200 TRP cc_start: 0.7948 (OUTLIER) cc_final: 0.7207 (m100) REVERT: i 37 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7942 (t) REVERT: i 39 GLU cc_start: 0.6162 (tt0) cc_final: 0.5825 (tt0) REVERT: i 63 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: m 109 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8290 (mmm-85) REVERT: s 34 TRP cc_start: 0.8540 (m100) cc_final: 0.8133 (m100) REVERT: s 74 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7466 (m-80) outliers start: 36 outliers final: 29 residues processed: 194 average time/residue: 0.1324 time to fit residues: 38.8655 Evaluate side-chains 211 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 63 TYR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 127 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 67 ASN ** g 68 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.123631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102915 restraints weight = 30986.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104463 restraints weight = 20169.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104833 restraints weight = 13956.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105054 restraints weight = 11996.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105189 restraints weight = 11178.721| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18274 Z= 0.179 Angle : 0.633 11.044 26924 Z= 0.321 Chirality : 0.037 0.279 3387 Planarity : 0.005 0.071 1703 Dihedral : 22.934 178.971 8174 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.92 % Allowed : 26.73 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.29), residues: 855 helix: 0.01 (0.31), residues: 308 sheet: -1.23 (0.48), residues: 127 loop : -2.71 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 87 TYR 0.010 0.001 TYR i 96 PHE 0.019 0.001 PHE s 44 TRP 0.027 0.002 TRP c 200 HIS 0.009 0.001 HIS c 99 Details of bonding type rmsd covalent geometry : bond 0.00362 (18274) covalent geometry : angle 0.63301 (26924) hydrogen bonds : bond 0.05629 ( 549) hydrogen bonds : angle 3.70901 ( 1172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.16 seconds wall clock time: 38 minutes 18.22 seconds (2298.22 seconds total)