Starting phenix.real_space_refine on Sat Sep 12 16:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bge_12179/09_2026/7bge_12179.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 465 5.49 5 S 21 5.16 5 C 8882 2.51 5 N 3119 2.21 5 O 4501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: 3.37, per 1000 atoms: 0.20 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: 1.47 Conformation dependent library (CDL) restraints added in 273.3 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: 2.15 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: 3.64 Time building geometry restraints manager: 1.96 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: 25005 2.87 - 5.74: 1768 5.74 - 8.61: 120 8.61 - 11.47: 25 11.47 - 14.34: 6 Bond angle restraints: 26924 Sorted by residual: angle pdb=" C3' U a1054 " pdb=" O3' U a1054 " pdb=" P G a1055 " ideal model delta sigma weight residual 119.70 129.45 -9.75 1.20e+00 6.94e-01 6.60e+01 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=" 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 - 29.70: 8676 29.70 - 59.39: 1199 59.39 - 89.09: 152 89.09 - 118.78: 0 118.78 - 148.48: 1 Dihedral angle restraints: 10028 sinusoidal: 7501 harmonic: 2527 Sorted by residual: dihedral pdb=" C4' U a1152 " pdb=" C3' U a1152 " pdb=" C2' U a1152 " pdb=" C1' U a1152 " ideal model delta sinusoidal sigma weight residual 36.34 -42.84 79.18 1 3.10e+00 1.04e-01 8.12e+02 dihedral pdb=" C4' G a1106 " pdb=" C3' G a1106 " pdb=" C2' G a1106 " pdb=" C1' G a1106 " ideal model delta sinusoidal sigma weight residual 36.34 -42.18 78.53 1 3.10e+00 1.04e-01 8.00e+02 dihedral pdb=" C4' U a1151 " pdb=" C3' U a1151 " pdb=" C2' U a1151 " pdb=" C1' U a1151 " ideal model delta sinusoidal sigma weight residual 36.34 -40.97 77.31 1 3.10e+00 1.04e-01 7.80e+02 ... (remaining 10025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2443 0.096 - 0.192: 323 0.192 - 0.288: 549 0.288 - 0.383: 66 0.383 - 0.479: 6 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 -2.50 -2.02 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C2' G a1171 " pdb=" C3' G a1171 " pdb=" O2' G a1171 " pdb=" C1' G a1171 " both_signs ideal model delta sigma weight residual False -2.79 -2.37 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" P U a 992 " pdb=" OP1 U a 992 " pdb=" OP2 U a 992 " pdb=" O5' U a 992 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.41 2.00e-01 2.50e+01 4.27e+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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.100 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- 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 : 0.007 0.061 18274 Z= 0.339 Angle : 1.513 14.342 26924 Z= 0.666 Chirality : 0.119 0.479 3387 Planarity : 0.009 0.115 1703 Dihedral : 21.488 148.476 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 0.00681 / 0.34 (18274) covalent geometry : angle 1.51287 / 0.67 (26924) hydrogen bonds : bond 0.15328 / 8.18 ( 549) hydrogen bonds : angle 6.78853 / 2.59 ( 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 : 0.406 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: 0.1594 time to fit residues: 61.1737 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 : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.131925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110768 restraints weight = 31161.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112732 restraints weight = 22009.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113711 restraints weight = 13002.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113698 restraints weight = 11094.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113844 restraints weight = 10097.431| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18274 Z= 0.219 Angle : 1.363 16.819 26924 Z= 0.546 Chirality : 0.112 0.951 3387 Planarity : 0.006 0.078 1703 Dihedral : 18.592 165.816 6569 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.93 % Allowed : 20.48 % Favored : 76.60 % 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: -2.46 (0.22), residues: 314 sheet: -1.94 (0.42), residues: 142 loop : -3.51 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG i 102 TYR 0.011 0.001 TYR n 21 PHE 0.017 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 0.00448 / 0.22 (18274) covalent geometry : angle 1.36262 / 0.55 (26924) hydrogen bonds : bond 0.08037 / 4.18 ( 549) hydrogen bonds : angle 4.19637 / 1.66 ( 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 213 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 99 HIS cc_start: 0.6668 (m-70) cc_final: 0.6450 (m170) REVERT: c 101 ASN cc_start: 0.8284 (t0) cc_final: 0.8065 (t0) REVERT: g 10 ARG cc_start: 0.5836 (pmt170) cc_final: 0.4910 (pmt-80) REVERT: g 116 MET cc_start: 0.8314 (tpt) cc_final: 0.8110 (tpt) outliers start: 22 outliers final: 10 residues processed: 203 average time/residue: 0.1285 time to fit residues: 38.7656 Evaluate side-chains 175 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain i residue 70 HIS Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain n residue 61 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 115 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS c 122 GLN g 67 ASN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112429 restraints weight = 31814.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114790 restraints weight = 20947.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115364 restraints weight = 12188.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115542 restraints weight = 10846.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115698 restraints weight = 9935.846| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18274 Z= 0.182 Angle : 1.128 14.975 26924 Z= 0.457 Chirality : 0.088 0.692 3387 Planarity : 0.005 0.069 1703 Dihedral : 18.542 171.730 6562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.99 % Allowed : 19.68 % Favored : 76.33 % 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: -3.18 (0.26), residues: 855 helix: -1.02 (0.28), residues: 310 sheet: -1.70 (0.44), residues: 132 loop : -3.19 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 102 TYR 0.009 0.001 TYR b 104 PHE 0.018 0.001 PHE s 44 TRP 0.027 0.002 TRP n 61 HIS 0.013 0.001 HIS i 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (18274) covalent geometry : angle 1.12765 / 0.46 (26924) hydrogen bonds : bond 0.07115 / 3.68 ( 549) hydrogen bonds : angle 3.70391 / 1.47 ( 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 205 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: c 122 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.6751 (mp-120) REVERT: c 200 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7173 (m100) REVERT: g 10 ARG cc_start: 0.6264 (pmt170) cc_final: 0.5744 (pmt-80) REVERT: i 47 ILE cc_start: 0.8004 (pt) cc_final: 0.7767 (mt) REVERT: i 66 LEU cc_start: 0.8655 (mt) cc_final: 0.8414 (mt) REVERT: j 27 GLU cc_start: 0.6183 (tm-30) cc_final: 0.5927 (tm-30) outliers start: 30 outliers final: 15 residues processed: 192 average time/residue: 0.1308 time to fit residues: 37.1352 Evaluate side-chains 183 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain c residue 122 GLN 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 131 THR Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN c 166 GLN g 142 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105187 restraints weight = 31495.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107464 restraints weight = 21197.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107710 restraints weight = 13146.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108100 restraints weight = 11623.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108171 restraints weight = 10445.934| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18274 Z= 0.255 Angle : 1.174 14.799 26924 Z= 0.478 Chirality : 0.091 0.784 3387 Planarity : 0.005 0.068 1703 Dihedral : 18.544 177.656 6562 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.85 % Allowed : 20.21 % Favored : 73.94 % 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: -0.64 (0.30), residues: 306 sheet: -1.69 (0.45), residues: 134 loop : -3.00 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 102 TYR 0.012 0.001 TYR n 21 PHE 0.019 0.002 PHE s 44 TRP 0.030 0.002 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (18274) covalent geometry : angle 1.17417 / 0.48 (26924) hydrogen bonds : bond 0.07063 / 3.68 ( 549) hydrogen bonds : angle 3.82424 / 1.52 ( 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 224 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 154 MET cc_start: 0.5286 (tpp) cc_final: 0.5059 (tpp) REVERT: b 189 THR cc_start: 0.3484 (OUTLIER) cc_final: 0.3155 (p) REVERT: c 118 ASN cc_start: 0.8541 (t0) cc_final: 0.7946 (t0) REVERT: c 200 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.7276 (m100) REVERT: g 15 ASP cc_start: 0.8022 (p0) cc_final: 0.7739 (p0) REVERT: i 77 GLN cc_start: 0.7781 (tt0) cc_final: 0.7527 (tt0) REVERT: m 25 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7059 (mp) REVERT: s 74 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7767 (m-80) outliers start: 44 outliers final: 22 residues processed: 205 average time/residue: 0.1305 time to fit residues: 40.1900 Evaluate side-chains 200 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU 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 131 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 112 MET 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 61 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.0770 chunk 50 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 166 GLN g 142 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111930 restraints weight = 31444.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113774 restraints weight = 22308.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114602 restraints weight = 13672.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114730 restraints weight = 12036.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114918 restraints weight = 10960.149| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18274 Z= 0.176 Angle : 1.075 15.630 26924 Z= 0.436 Chirality : 0.084 0.590 3387 Planarity : 0.005 0.064 1703 Dihedral : 18.568 178.754 6562 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.99 % Allowed : 23.54 % Favored : 72.47 % 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: -0.22 (0.31), residues: 295 sheet: -1.59 (0.45), residues: 138 loop : -2.83 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG i 102 TYR 0.006 0.001 TYR m 21 PHE 0.018 0.001 PHE s 44 TRP 0.025 0.002 TRP c 200 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (18274) covalent geometry : angle 1.07504 / 0.44 (26924) hydrogen bonds : bond 0.06656 / 3.42 ( 549) hydrogen bonds : angle 3.55943 / 1.42 ( 1172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 122 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: c 200 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7143 (m100) REVERT: g 15 ASP cc_start: 0.7842 (p0) cc_final: 0.7623 (p0) REVERT: j 27 GLU cc_start: 0.6316 (tm-30) cc_final: 0.6091 (tm-30) REVERT: j 53 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.8044 (mtp85) REVERT: m 25 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6868 (mp) REVERT: m 109 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8187 (mmm-85) REVERT: s 34 TRP cc_start: 0.8441 (m100) cc_final: 0.8067 (m100) REVERT: s 74 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7398 (m-80) outliers start: 30 outliers final: 17 residues processed: 210 average time/residue: 0.1286 time to fit residues: 39.8979 Evaluate side-chains 200 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU 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 s residue 74 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 3 GLN c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN g 67 ASN g 142 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106422 restraints weight = 31509.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107744 restraints weight = 23967.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108380 restraints weight = 16950.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108511 restraints weight = 13467.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108604 restraints weight = 12338.864| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18274 Z= 0.253 Angle : 1.145 15.479 26924 Z= 0.466 Chirality : 0.088 0.674 3387 Planarity : 0.006 0.066 1703 Dihedral : 18.553 178.515 6562 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 5.72 % Allowed : 23.80 % 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: -2.47 (0.28), residues: 855 helix: -0.23 (0.31), residues: 300 sheet: -1.60 (0.46), residues: 138 loop : -2.80 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG i 102 TYR 0.011 0.001 TYR n 21 PHE 0.018 0.002 PHE s 44 TRP 0.029 0.002 TRP c 200 HIS 0.006 0.001 HIS s 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (18274) covalent geometry : angle 1.14535 / 0.47 (26924) hydrogen bonds : bond 0.06905 / 3.58 ( 549) hydrogen bonds : angle 3.75723 / 1.50 ( 1172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 100 LEU cc_start: 0.8117 (pp) cc_final: 0.7885 (pp) REVERT: b 189 THR cc_start: 0.3316 (OUTLIER) cc_final: 0.3063 (p) REVERT: c 122 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: c 200 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7258 (m100) REVERT: g 15 ASP cc_start: 0.7878 (p0) cc_final: 0.7648 (p0) REVERT: i 37 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8298 (t) REVERT: i 49 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.5903 (m-30) REVERT: m 25 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7000 (mp) REVERT: m 109 ARG cc_start: 0.8518 (mtp85) cc_final: 0.8233 (mmm-85) REVERT: s 34 TRP cc_start: 0.8455 (m100) cc_final: 0.8208 (m100) REVERT: s 74 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7703 (m-80) outliers start: 43 outliers final: 26 residues processed: 212 average time/residue: 0.1307 time to fit residues: 41.5305 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 : 0.304 ------------------------------------------------------------------------------- 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 b residue 189 THR 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 122 GLN 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 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 6 ASN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 118 ASN c 166 GLN g 67 ASN g 142 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106206 restraints weight = 31367.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107734 restraints weight = 22756.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108069 restraints weight = 17225.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108256 restraints weight = 14045.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108352 restraints weight = 12660.228| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18274 Z= 0.248 Angle : 1.140 15.302 26924 Z= 0.464 Chirality : 0.087 0.635 3387 Planarity : 0.005 0.066 1703 Dihedral : 18.561 179.391 6562 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.72 % Allowed : 23.54 % Favored : 70.74 % 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: -0.28 (0.31), residues: 310 sheet: -1.61 (0.46), residues: 138 loop : -2.84 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 102 TYR 0.011 0.001 TYR n 21 PHE 0.019 0.002 PHE s 44 TRP 0.029 0.002 TRP c 200 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (18274) covalent geometry : angle 1.13980 / 0.46 (26924) hydrogen bonds : bond 0.06875 / 3.55 ( 549) hydrogen bonds : angle 3.76805 / 1.50 ( 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 220 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 131 LYS cc_start: 0.7081 (tppt) cc_final: 0.6583 (tppt) REVERT: b 189 THR cc_start: 0.3343 (OUTLIER) cc_final: 0.3100 (p) REVERT: c 122 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: c 200 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.7201 (m100) REVERT: j 24 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7678 (ttpt) REVERT: m 109 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8242 (mmm-85) REVERT: s 34 TRP cc_start: 0.8494 (m100) cc_final: 0.8253 (m100) REVERT: s 74 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7694 (m-80) outliers start: 43 outliers final: 28 residues processed: 201 average time/residue: 0.1281 time to fit residues: 38.8800 Evaluate side-chains 210 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP 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 18 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain 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 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: 9.9990 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN g 142 HIS j 15 HIS ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108410 restraints weight = 31631.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110168 restraints weight = 22573.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110460 restraints weight = 16447.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110622 restraints weight = 13430.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110717 restraints weight = 12092.115| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18274 Z= 0.196 Angle : 1.104 15.575 26924 Z= 0.449 Chirality : 0.085 0.592 3387 Planarity : 0.005 0.066 1703 Dihedral : 18.552 179.827 6562 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 5.45 % Allowed : 24.87 % Favored : 69.68 % 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: -2.44 (0.29), residues: 855 helix: -0.18 (0.31), residues: 312 sheet: -1.51 (0.46), residues: 136 loop : -2.89 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG i 102 TYR 0.006 0.001 TYR n 21 PHE 0.018 0.001 PHE s 44 TRP 0.027 0.001 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (18274) covalent geometry : angle 1.10358 / 0.45 (26924) hydrogen bonds : bond 0.06674 / 3.44 ( 549) hydrogen bonds : angle 3.69527 / 1.48 ( 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 211 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3318 (OUTLIER) cc_final: 0.3083 (p) REVERT: c 122 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: c 200 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.7157 (m100) REVERT: m 25 ILE cc_start: 0.7333 (mp) cc_final: 0.7083 (mp) REVERT: n 6 MET cc_start: 0.8758 (mmt) cc_final: 0.8509 (mmt) REVERT: s 34 TRP cc_start: 0.8469 (m100) cc_final: 0.8251 (m100) REVERT: s 74 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7702 (m-80) outliers start: 41 outliers final: 28 residues processed: 192 average time/residue: 0.1260 time to fit residues: 36.7841 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 : 0.275 ------------------------------------------------------------------------------- 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 51 VAL Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 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 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 109 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 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 16 MET 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: 2.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 g 142 HIS ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106892 restraints weight = 31416.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108454 restraints weight = 22089.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108847 restraints weight = 15879.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108971 restraints weight = 13304.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109127 restraints weight = 12144.553| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18274 Z= 0.239 Angle : 1.137 15.529 26924 Z= 0.462 Chirality : 0.086 0.617 3387 Planarity : 0.005 0.067 1703 Dihedral : 18.533 179.576 6562 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.05 % Allowed : 25.80 % Favored : 69.15 % 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: -2.34 (0.29), residues: 855 helix: -0.06 (0.31), residues: 307 sheet: -1.45 (0.47), residues: 135 loop : -2.85 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG i 102 TYR 0.009 0.001 TYR n 21 PHE 0.019 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 0.00503 / 0.24 (18274) covalent geometry : angle 1.13685 / 0.46 (26924) hydrogen bonds : bond 0.06836 / 3.54 ( 549) hydrogen bonds : angle 3.80378 / 1.52 ( 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 215 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3518 (OUTLIER) cc_final: 0.3307 (p) REVERT: c 122 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: c 200 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.7277 (m100) REVERT: m 109 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8242 (mmm-85) REVERT: n 6 MET cc_start: 0.8733 (mmt) cc_final: 0.8486 (mmt) REVERT: s 34 TRP cc_start: 0.8477 (m100) cc_final: 0.8167 (m100) REVERT: s 74 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7873 (m-80) outliers start: 38 outliers final: 28 residues processed: 198 average time/residue: 0.1358 time to fit residues: 40.1356 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 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 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 40 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 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: 3.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN g 40 GLN g 142 HIS ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110264 restraints weight = 31153.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112337 restraints weight = 21684.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112875 restraints weight = 13228.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113109 restraints weight = 11608.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113197 restraints weight = 10585.068| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4910 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= 0.177 Angle : 1.081 15.839 26924 Z= 0.439 Chirality : 0.083 0.635 3387 Planarity : 0.005 0.067 1703 Dihedral : 18.552 179.281 6562 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.86 % Allowed : 26.60 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.29), residues: 855 helix: -0.04 (0.31), residues: 312 sheet: -1.40 (0.47), residues: 136 loop : -2.74 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG i 102 TYR 0.006 0.001 TYR n 49 PHE 0.016 0.001 PHE s 44 TRP 0.025 0.001 TRP c 200 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (18274) covalent geometry : angle 1.08121 / 0.44 (26924) hydrogen bonds : bond 0.06585 / 3.38 ( 549) hydrogen bonds : angle 3.65584 / 1.46 ( 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 208 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3585 (OUTLIER) cc_final: 0.3368 (p) REVERT: c 122 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: c 200 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7113 (m100) REVERT: i 39 GLU cc_start: 0.5949 (tt0) cc_final: 0.5695 (tt0) REVERT: m 25 ILE cc_start: 0.7401 (mp) cc_final: 0.7178 (mp) REVERT: m 95 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.5033 (tp) REVERT: m 109 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8189 (mmm-85) REVERT: n 6 MET cc_start: 0.8744 (mmt) cc_final: 0.8509 (mmp) REVERT: s 34 TRP cc_start: 0.8438 (m100) cc_final: 0.8149 (m100) REVERT: s 74 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7664 (m-80) outliers start: 29 outliers final: 23 residues processed: 194 average time/residue: 0.1317 time to fit residues: 38.1229 Evaluate side-chains 200 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** s 22 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111090 restraints weight = 31321.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112598 restraints weight = 23653.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113251 restraints weight = 16147.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113382 restraints weight = 13083.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113483 restraints weight = 11855.228| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18274 Z= 0.188 Angle : 1.077 16.163 26924 Z= 0.437 Chirality : 0.081 0.624 3387 Planarity : 0.005 0.067 1703 Dihedral : 18.514 179.194 6562 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.86 % Allowed : 27.26 % Favored : 68.88 % 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: -2.21 (0.29), residues: 855 helix: 0.11 (0.32), residues: 304 sheet: -1.17 (0.46), residues: 146 loop : -2.92 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG i 102 TYR 0.013 0.001 TYR c 23 PHE 0.016 0.001 PHE s 44 TRP 0.025 0.001 TRP c 200 HIS 0.005 0.001 HIS j 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (18274) covalent geometry : angle 1.07718 / 0.44 (26924) hydrogen bonds : bond 0.06556 / 3.37 ( 549) hydrogen bonds : angle 3.61510 / 1.44 ( 1172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2242.29 seconds wall clock time: 39 minutes 55.79 seconds (2395.79 seconds total)