Starting phenix.real_space_refine on Fri Jul 3 23:23:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bge_12179/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bge_12179/07_2026/7bge_12179.map" } 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-6108/lib/python3.11/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: 3.59, per 1000 atoms: 0.21 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: 1.23 Conformation dependent library (CDL) restraints added in 420.9 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: 2.17 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: 3.67 Time building geometry restraints manager: 1.78 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: 9548 35.70 - 71.40: 440 71.40 - 107.10: 34 107.10 - 142.80: 1 142.80 - 178.50: 5 Dihedral angle restraints: 10028 sinusoidal: 7501 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 10025 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 16.632 178.504 8396 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/Z covalent geometry : bond 0.00649 / 0.34 (18274) covalent geometry : angle 1.32928 / 0.65 (26924) hydrogen bonds : bond 0.15328 / 9.32 ( 549) hydrogen bonds : angle 6.78853 / 3.67 ( 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 : 0.395 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: 0.1740 time to fit residues: 66.9862 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 : 0.365 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3730 r_free = 0.3730 target = 0.129691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108352 restraints weight = 30896.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110295 restraints weight = 22595.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110589 restraints weight = 13732.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110955 restraints weight = 12409.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111020 restraints weight = 11727.217| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2295 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= 0.152 Angle : 0.634 7.939 26924 Z= 0.332 Chirality : 0.037 0.240 3387 Planarity : 0.006 0.075 1703 Dihedral : 15.143 178.716 6569 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % 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: -4.28 (0.23), residues: 855 helix: -2.45 (0.22), residues: 315 sheet: -1.90 (0.42), residues: 142 loop : -3.55 (0.25), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 90 TYR 0.011 0.001 TYR n 21 PHE 0.016 0.001 PHE s 44 TRP 0.028 0.001 TRP c 200 HIS 0.005 0.001 HIS i 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (18274) covalent geometry : angle 0.63443 / 0.33 (26924) hydrogen bonds : bond 0.06198 / 3.78 ( 549) hydrogen bonds : angle 4.11553 / 2.33 ( 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 : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 101 ASN cc_start: 0.8266 (t0) cc_final: 0.8040 (t0) REVERT: g 10 ARG cc_start: 0.5893 (pmt170) cc_final: 0.4921 (pmt-80) REVERT: i 105 LEU cc_start: 0.8973 (mp) cc_final: 0.8760 (mp) REVERT: s 27 LYS cc_start: 0.6042 (mttm) cc_final: 0.5801 (mtmm) REVERT: s 34 TRP cc_start: 0.8501 (m100) cc_final: 0.8043 (m100) outliers start: 22 outliers final: 7 residues processed: 207 average time/residue: 0.1342 time to fit residues: 41.5837 Evaluate side-chains 173 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 67 ASN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095710 restraints weight = 31745.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097917 restraints weight = 23935.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097968 restraints weight = 14112.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098121 restraints weight = 13292.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098214 restraints weight = 12179.894| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 18274 Z= 0.343 Angle : 0.781 11.239 26924 Z= 0.398 Chirality : 0.043 0.275 3387 Planarity : 0.006 0.072 1703 Dihedral : 15.187 177.956 6562 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.28 % Favored : 87.60 % Rotamer: Outliers : 5.59 % Allowed : 18.88 % Favored : 75.53 % 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: -3.46 (0.25), residues: 855 helix: -1.23 (0.28), residues: 306 sheet: -2.01 (0.42), residues: 133 loop : -3.30 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG i 102 TYR 0.018 0.002 TYR b 104 PHE 0.025 0.002 PHE s 44 TRP 0.036 0.003 TRP c 200 HIS 0.006 0.002 HIS c 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.34 (18274) covalent geometry : angle 0.78121 / 0.40 (26924) hydrogen bonds : bond 0.07255 / 4.41 ( 549) hydrogen bonds : angle 4.25646 / 2.38 ( 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 218 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3552 (OUTLIER) cc_final: 0.3223 (p) REVERT: c 45 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: c 118 ASN cc_start: 0.8326 (t0) cc_final: 0.7754 (t0) REVERT: c 151 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: c 200 TRP cc_start: 0.8059 (OUTLIER) cc_final: 0.7426 (m100) REVERT: g 15 ASP cc_start: 0.7960 (p0) cc_final: 0.7675 (p0) REVERT: g 51 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6595 (mm-30) REVERT: i 47 ILE cc_start: 0.8369 (pt) cc_final: 0.8050 (mp) REVERT: i 77 GLN cc_start: 0.7937 (tt0) cc_final: 0.7702 (tt0) REVERT: i 115 ARG cc_start: 0.7077 (ptp-170) cc_final: 0.6811 (ptp90) REVERT: j 24 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7434 (ttpt) REVERT: j 27 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6079 (tm-30) REVERT: s 16 MET cc_start: 0.7358 (tpt) cc_final: 0.7132 (tpt) REVERT: s 74 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7784 (m-80) outliers start: 42 outliers final: 20 residues processed: 200 average time/residue: 0.1419 time to fit residues: 42.1773 Evaluate side-chains 183 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 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 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 30 VAL 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: 0.9990 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3666 r_free = 0.3666 target = 0.125368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104390 restraints weight = 31051.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106618 restraints weight = 21758.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107490 restraints weight = 13390.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107404 restraints weight = 12616.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107554 restraints weight = 10588.465| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18274 Z= 0.149 Angle : 0.604 10.193 26924 Z= 0.313 Chirality : 0.036 0.260 3387 Planarity : 0.005 0.067 1703 Dihedral : 14.963 179.521 6562 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.39 % Allowed : 23.54 % Favored : 72.07 % 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: -2.84 (0.27), residues: 855 helix: -0.43 (0.30), residues: 300 sheet: -1.93 (0.43), residues: 138 loop : -3.05 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 102 TYR 0.006 0.001 TYR n 21 PHE 0.019 0.001 PHE s 44 TRP 0.024 0.001 TRP c 200 HIS 0.003 0.001 HIS c 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (18274) covalent geometry : angle 0.60369 / 0.31 (26924) hydrogen bonds : bond 0.05719 / 3.47 ( 549) hydrogen bonds : angle 3.73253 / 2.18 ( 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 214 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7123 (m100) REVERT: g 15 ASP cc_start: 0.7970 (p0) cc_final: 0.7737 (p0) REVERT: i 49 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6095 (m-30) REVERT: j 82 LYS cc_start: 0.7819 (mppt) cc_final: 0.7475 (mtmm) REVERT: m 25 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6393 (mp) REVERT: s 34 TRP cc_start: 0.8485 (m100) cc_final: 0.8053 (m100) outliers start: 33 outliers final: 16 residues processed: 198 average time/residue: 0.1354 time to fit residues: 39.9582 Evaluate side-chains 188 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 200 TRP 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 96 VAL Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS c 151 GLN n 11 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.126967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105821 restraints weight = 31095.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108009 restraints weight = 22438.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108136 restraints weight = 13221.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108356 restraints weight = 12163.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108465 restraints weight = 11301.911| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18274 Z= 0.135 Angle : 0.582 12.021 26924 Z= 0.299 Chirality : 0.035 0.265 3387 Planarity : 0.004 0.068 1703 Dihedral : 14.806 179.975 6562 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.05 % Allowed : 24.47 % Favored : 70.48 % 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: -2.50 (0.28), residues: 855 helix: -0.20 (0.31), residues: 303 sheet: -1.69 (0.44), residues: 138 loop : -2.84 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 102 TYR 0.012 0.001 TYR c 23 PHE 0.015 0.001 PHE s 44 TRP 0.025 0.001 TRP c 200 HIS 0.004 0.001 HIS c 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (18274) covalent geometry : angle 0.58158 / 0.30 (26924) hydrogen bonds : bond 0.05383 / 3.27 ( 549) hydrogen bonds : angle 3.56652 / 2.09 ( 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 221 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 45 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7038 (pt0) REVERT: c 200 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.7057 (m100) REVERT: g 15 ASP cc_start: 0.7925 (p0) cc_final: 0.7628 (p0) REVERT: g 51 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6900 (mm-30) REVERT: m 25 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6366 (mp) REVERT: n 6 MET cc_start: 0.8596 (mmt) cc_final: 0.8365 (mmt) REVERT: s 34 TRP cc_start: 0.8439 (m100) cc_final: 0.8060 (m100) outliers start: 38 outliers final: 24 residues processed: 205 average time/residue: 0.1303 time to fit residues: 40.3722 Evaluate side-chains 197 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 6 ASN 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 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 131 THR Chi-restraints excluded: chain i residue 49 ASP 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 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 27 LYS Chi-restraints excluded: chain s residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 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: 0.8980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN g 67 ASN i 128 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096386 restraints weight = 31545.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096812 restraints weight = 21446.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098665 restraints weight = 18363.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098611 restraints weight = 12764.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098729 restraints weight = 11443.081| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 18274 Z= 0.336 Angle : 0.774 18.896 26924 Z= 0.390 Chirality : 0.043 0.314 3387 Planarity : 0.006 0.070 1703 Dihedral : 15.055 178.168 6562 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 6.78 % Allowed : 24.60 % Favored : 68.62 % 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: -2.71 (0.28), residues: 855 helix: -0.45 (0.31), residues: 302 sheet: -1.61 (0.45), residues: 134 loop : -2.97 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG i 102 TYR 0.015 0.002 TYR n 21 PHE 0.029 0.002 PHE s 74 TRP 0.036 0.002 TRP c 200 HIS 0.005 0.001 HIS i 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.34 (18274) covalent geometry : angle 0.77361 / 0.39 (26924) hydrogen bonds : bond 0.07066 / 4.30 ( 549) hydrogen bonds : angle 4.14860 / 2.41 ( 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 231 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: b 100 LEU cc_start: 0.8338 (pp) cc_final: 0.8138 (pp) REVERT: c 118 ASN cc_start: 0.8194 (t0) cc_final: 0.6373 (t0) REVERT: c 122 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.6633 (mp-120) REVERT: c 126 ARG cc_start: 0.7885 (ptt180) cc_final: 0.7584 (ptt180) REVERT: c 200 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7350 (m100) REVERT: g 15 ASP cc_start: 0.8027 (p0) cc_final: 0.7774 (p0) REVERT: i 115 ARG cc_start: 0.6877 (ptp-170) cc_final: 0.6665 (ptp90) REVERT: m 109 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8473 (mtp85) REVERT: s 34 TRP cc_start: 0.8649 (m100) cc_final: 0.8272 (m100) REVERT: s 74 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7880 (m-80) outliers start: 51 outliers final: 30 residues processed: 210 average time/residue: 0.1324 time to fit residues: 41.3212 Evaluate side-chains 202 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 108 VAL Chi-restraints excluded: chain c residue 122 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 66 ILE 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 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 14 ASP 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 30 VAL 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: 6.9990 chunk 86 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** j 15 HIS ** 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 = 0.3612 r_free = 0.3612 target = 0.121608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100300 restraints weight = 31086.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102639 restraints weight = 21905.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102631 restraints weight = 13538.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102977 restraints weight = 12113.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102998 restraints weight = 11204.013| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18274 Z= 0.188 Angle : 0.642 12.157 26924 Z= 0.329 Chirality : 0.038 0.261 3387 Planarity : 0.005 0.067 1703 Dihedral : 14.920 178.707 6562 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 4.52 % Allowed : 26.46 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.29), residues: 855 helix: -0.25 (0.31), residues: 306 sheet: -1.76 (0.45), residues: 138 loop : -2.92 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 102 TYR 0.008 0.001 TYR i 96 PHE 0.020 0.002 PHE s 44 TRP 0.028 0.001 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (18274) covalent geometry : angle 0.64202 / 0.33 (26924) hydrogen bonds : bond 0.05887 / 3.59 ( 549) hydrogen bonds : angle 3.81519 / 2.23 ( 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 219 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: b 100 LEU cc_start: 0.8302 (pp) cc_final: 0.7948 (pp) REVERT: b 131 LYS cc_start: 0.7269 (tppt) cc_final: 0.6740 (tppt) REVERT: c 126 ARG cc_start: 0.7805 (ptt180) cc_final: 0.7581 (ptt180) REVERT: c 200 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.7176 (m100) REVERT: g 15 ASP cc_start: 0.7988 (p0) cc_final: 0.7733 (p0) REVERT: g 51 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6841 (mm-30) REVERT: i 39 GLU cc_start: 0.6165 (tt0) cc_final: 0.5837 (tt0) REVERT: m 109 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8298 (mmm-85) REVERT: s 27 LYS cc_start: 0.6327 (mtpt) cc_final: 0.6077 (mtpp) REVERT: s 34 TRP cc_start: 0.8578 (m100) cc_final: 0.8257 (m100) REVERT: s 74 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7787 (m-80) outliers start: 34 outliers final: 24 residues processed: 203 average time/residue: 0.1413 time to fit residues: 42.5556 Evaluate side-chains 197 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE 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 108 VAL 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 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP 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 14 ASP 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 Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100264 restraints weight = 31416.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102901 restraints weight = 22179.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102791 restraints weight = 13275.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102982 restraints weight = 11915.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103036 restraints weight = 11057.514| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4057 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= 0.201 Angle : 0.650 13.164 26924 Z= 0.330 Chirality : 0.038 0.260 3387 Planarity : 0.005 0.069 1703 Dihedral : 14.900 178.657 6562 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.70 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: -2.50 (0.29), residues: 855 helix: -0.37 (0.30), residues: 316 sheet: -1.67 (0.45), residues: 137 loop : -2.77 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG c 62 TYR 0.017 0.001 TYR b 104 PHE 0.020 0.002 PHE s 74 TRP 0.028 0.002 TRP c 200 HIS 0.005 0.001 HIS s 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (18274) covalent geometry : angle 0.64997 / 0.33 (26924) hydrogen bonds : bond 0.05858 / 3.57 ( 549) hydrogen bonds : angle 3.82952 / 2.23 ( 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 212 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 126 ARG cc_start: 0.7797 (ptt180) cc_final: 0.7551 (ptt180) REVERT: c 200 TRP cc_start: 0.7949 (OUTLIER) cc_final: 0.7194 (m100) REVERT: g 15 ASP cc_start: 0.8014 (p0) cc_final: 0.7776 (p0) REVERT: i 39 GLU cc_start: 0.6157 (tt0) cc_final: 0.5851 (tt0) REVERT: m 25 ILE cc_start: 0.7450 (mp) cc_final: 0.7248 (mp) REVERT: m 109 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8293 (mmm-85) REVERT: s 34 TRP cc_start: 0.8584 (m100) cc_final: 0.8156 (m100) REVERT: s 74 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7635 (m-80) outliers start: 37 outliers final: 28 residues processed: 197 average time/residue: 0.1438 time to fit residues: 42.3103 Evaluate side-chains 202 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 ASN 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 93 LEU Chi-restraints excluded: chain c residue 108 VAL 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 117 GLU Chi-restraints excluded: chain g residue 131 THR 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 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 80 THR 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 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: 0.8980 chunk 106 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS 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 = 0.121693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100401 restraints weight = 31184.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102977 restraints weight = 21725.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102821 restraints weight = 13776.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103010 restraints weight = 12515.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103057 restraints weight = 11134.132| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4113 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= 0.200 Angle : 0.652 13.188 26924 Z= 0.330 Chirality : 0.038 0.263 3387 Planarity : 0.005 0.069 1703 Dihedral : 14.890 178.686 6562 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 4.79 % Allowed : 26.86 % 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: -2.43 (0.29), residues: 855 helix: -0.25 (0.31), residues: 312 sheet: -1.43 (0.45), residues: 141 loop : -2.87 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG i 102 TYR 0.013 0.001 TYR b 104 PHE 0.020 0.002 PHE s 44 TRP 0.028 0.002 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (18274) covalent geometry : angle 0.65220 / 0.33 (26924) hydrogen bonds : bond 0.05827 / 3.56 ( 549) hydrogen bonds : angle 3.81013 / 2.22 ( 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 213 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 126 ARG cc_start: 0.7783 (ptt180) cc_final: 0.7571 (ptt180) REVERT: c 200 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7157 (m100) REVERT: i 39 GLU cc_start: 0.6182 (tt0) cc_final: 0.5880 (tt0) REVERT: i 63 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: j 27 GLU cc_start: 0.6363 (tm-30) cc_final: 0.6131 (tm-30) REVERT: m 109 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8322 (mmm-85) REVERT: s 34 TRP cc_start: 0.8580 (m100) cc_final: 0.8152 (m100) REVERT: s 74 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7649 (m-80) outliers start: 36 outliers final: 29 residues processed: 198 average time/residue: 0.1357 time to fit residues: 40.2389 Evaluate side-chains 202 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 c residue 6 ASN 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 108 VAL Chi-restraints excluded: chain c residue 153 SER 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 117 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 49 ASP 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 80 THR 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 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: 0.9980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 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: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 91 HIS ** 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 = 0.3609 r_free = 0.3609 target = 0.121541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100273 restraints weight = 31033.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103001 restraints weight = 21680.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102809 restraints weight = 13024.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103000 restraints weight = 11843.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103071 restraints weight = 10799.309| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18274 Z= 0.203 Angle : 0.651 10.781 26924 Z= 0.330 Chirality : 0.038 0.265 3387 Planarity : 0.005 0.069 1703 Dihedral : 14.887 178.538 6562 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.35 % Favored : 88.54 % Rotamer: Outliers : 4.39 % Allowed : 26.99 % Favored : 68.62 % 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: -2.45 (0.29), residues: 855 helix: -0.34 (0.31), residues: 317 sheet: -1.44 (0.44), residues: 142 loop : -2.83 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG i 102 TYR 0.013 0.001 TYR b 104 PHE 0.020 0.002 PHE s 74 TRP 0.028 0.002 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (18274) covalent geometry : angle 0.65090 / 0.33 (26924) hydrogen bonds : bond 0.05822 / 3.55 ( 549) hydrogen bonds : angle 3.82526 / 2.22 ( 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 204 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 126 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7577 (ptt180) REVERT: c 200 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.7179 (m100) REVERT: g 51 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6860 (mm-30) REVERT: i 39 GLU cc_start: 0.6188 (tt0) cc_final: 0.5888 (tt0) REVERT: i 63 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: j 27 GLU cc_start: 0.6257 (tm-30) cc_final: 0.6015 (tm-30) REVERT: m 109 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8320 (mmm-85) REVERT: s 34 TRP cc_start: 0.8586 (m100) cc_final: 0.8147 (m100) REVERT: s 74 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7604 (m-80) outliers start: 33 outliers final: 29 residues processed: 190 average time/residue: 0.1366 time to fit residues: 38.4592 Evaluate side-chains 201 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 c residue 6 ASN 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 108 VAL Chi-restraints excluded: chain c residue 153 SER 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 117 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 49 ASP 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 80 THR 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 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: 0.6980 chunk 123 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096005 restraints weight = 31259.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097685 restraints weight = 22978.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098029 restraints weight = 15899.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098125 restraints weight = 13387.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098212 restraints weight = 12558.611| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 18274 Z= 0.305 Angle : 0.753 12.233 26924 Z= 0.379 Chirality : 0.042 0.262 3387 Planarity : 0.006 0.070 1703 Dihedral : 15.043 177.536 6562 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 4.65 % Allowed : 25.93 % Favored : 69.41 % 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: -2.57 (0.28), residues: 855 helix: -0.38 (0.30), residues: 313 sheet: -1.34 (0.43), residues: 152 loop : -3.04 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG m 90 TYR 0.016 0.002 TYR b 104 PHE 0.026 0.002 PHE s 44 TRP 0.034 0.002 TRP c 200 HIS 0.005 0.001 HIS c 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.30 (18274) covalent geometry : angle 0.75304 / 0.38 (26924) hydrogen bonds : bond 0.06756 / 4.12 ( 549) hydrogen bonds : angle 4.06866 / 2.34 ( 1172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.87 seconds wall clock time: 39 minutes 28.83 seconds (2368.83 seconds total)