Starting phenix.real_space_refine on Fri Jul 3 02:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.map" model { file = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2026/7z0o_14428.cif" } resolution = 2.8 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= 0.001 sd= 0.019 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 78 5.49 5 S 29 5.16 5 C 7291 2.51 5 N 2111 2.21 5 O 2355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11864 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2436 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 5 Chain: "E" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2518 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1067 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 2 Chain: "G" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "H" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1380 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 166} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 820 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 779 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Time building chain proxies: 2.77, per 1000 atoms: 0.23 Number of scatterers: 11864 At special positions: 0 Unit cell: (74.175, 126.42, 132.225, 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 29 16.00 P 78 15.00 O 2355 8.00 N 2111 7.00 C 7291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 397.6 milliseconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 64.8% alpha, 6.0% beta 36 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.695A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.526A pdb=" N ILE A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.508A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.662A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.562A pdb=" N SER B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.603A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.621A pdb=" N ASP C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 115 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.581A pdb=" N ILE C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.501A pdb=" N TRP D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 93 through 110 Processing helix chain 'D' and resid 128 through 147 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.893A pdb=" N TRP D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 195 through 218 Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.521A pdb=" N ALA D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.679A pdb=" N VAL D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 340 through 363 Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.566A pdb=" N ASP E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 129 through 160 Processing helix chain 'E' and resid 171 through 208 Processing helix chain 'E' and resid 229 through 240 Processing helix chain 'E' and resid 244 through 256 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.700A pdb=" N ARG E 268 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.529A pdb=" N LYS E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 340 Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 67 through 83 Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.937A pdb=" N ILE F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 91 through 109 removed outlier: 3.772A pdb=" N TYR F 109 " --> pdb=" O TRP F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 132 removed outlier: 4.460A pdb=" N CYS F 129 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.608A pdb=" N MET G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.569A pdb=" N LYS G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.878A pdb=" N LEU G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 86 removed outlier: 3.581A pdb=" N GLU G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 128 through 146 Processing helix chain 'H' and resid 173 through 179 removed outlier: 3.945A pdb=" N PHE H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 236 Proline residue: H 232 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.665A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 41 removed outlier: 4.121A pdb=" N LEU D 187 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA8, first strand: chain 'F' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'H' and resid 102 through 106 removed outlier: 3.627A pdb=" N MET H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 111 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU H 67 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY H 162 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN H 69 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE H 160 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL H 71 " --> pdb=" O GLN H 158 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR H 75 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP H 154 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE H 160 " --> pdb=" O GLY H 216 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY H 216 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 202 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET H 197 " --> pdb=" O ILE H 202 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3656 1.34 - 1.46: 3057 1.46 - 1.58: 5318 1.58 - 1.70: 154 1.70 - 1.82: 46 Bond restraints: 12231 Sorted by residual: bond pdb=" C3' DA T 71 " pdb=" O3' DA T 71 " ideal model delta sigma weight residual 1.435 1.409 0.026 1.30e-02 5.92e+03 3.94e+00 bond pdb=" C3' DA N -82 " pdb=" C2' DA N -82 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 3.89e+00 bond pdb=" C3' DA T 70 " pdb=" O3' DA T 70 " ideal model delta sigma weight residual 1.435 1.410 0.025 1.30e-02 5.92e+03 3.80e+00 bond pdb=" C3' DT N -60 " pdb=" O3' DT N -60 " ideal model delta sigma weight residual 1.435 1.410 0.025 1.30e-02 5.92e+03 3.64e+00 bond pdb=" C3' DA N -62 " pdb=" O3' DA N -62 " ideal model delta sigma weight residual 1.435 1.410 0.025 1.30e-02 5.92e+03 3.64e+00 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16441 1.92 - 3.84: 275 3.84 - 5.76: 84 5.76 - 7.68: 6 7.68 - 9.60: 2 Bond angle restraints: 16808 Sorted by residual: angle pdb=" O4' DC T 79 " pdb=" C4' DC T 79 " pdb=" C3' DC T 79 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" C4' DG N -59 " pdb=" O4' DG N -59 " pdb=" C1' DG N -59 " ideal model delta sigma weight residual 110.10 104.92 5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" C4' DT T 85 " pdb=" O4' DT T 85 " pdb=" C1' DT T 85 " ideal model delta sigma weight residual 110.10 105.19 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" O4' DA N -90 " pdb=" C4' DA N -90 " pdb=" C3' DA N -90 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" C4' DT T 87 " pdb=" O4' DT T 87 " pdb=" C1' DT T 87 " ideal model delta sigma weight residual 110.10 105.27 4.83 1.00e+00 1.00e+00 2.34e+01 ... (remaining 16803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6040 18.08 - 36.15: 825 36.15 - 54.22: 364 54.22 - 72.30: 87 72.30 - 90.37: 14 Dihedral angle restraints: 7330 sinusoidal: 3614 harmonic: 3716 Sorted by residual: dihedral pdb=" CA SER D 41 " pdb=" C SER D 41 " pdb=" N ILE D 42 " pdb=" CA ILE D 42 " ideal model delta harmonic sigma weight residual 180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS F 126 " pdb=" C LYS F 126 " pdb=" N GLY F 127 " pdb=" CA GLY F 127 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " pdb=" CZ ARG H 98 " ideal model delta sinusoidal sigma weight residual 90.00 41.51 48.49 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 7327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1294 0.032 - 0.064: 387 0.064 - 0.097: 160 0.097 - 0.129: 53 0.129 - 0.161: 3 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CB ILE D 42 " pdb=" CA ILE D 42 " pdb=" CG1 ILE D 42 " pdb=" CG2 ILE D 42 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA GLN G 43 " pdb=" N GLN G 43 " pdb=" C GLN G 43 " pdb=" CB GLN G 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ASP D 261 " pdb=" N ASP D 261 " pdb=" C ASP D 261 " pdb=" CB ASP D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1894 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 168 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO H 169 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 169 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 169 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 61 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO G 62 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 28 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CD GLN B 28 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 28 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 11598 3.27 - 3.82: 20751 3.82 - 4.36: 25016 4.36 - 4.90: 40566 Nonbonded interactions: 98618 Sorted by model distance: nonbonded pdb=" OG SER G 42 " pdb=" OE1 GLN G 43 " model vdw 2.189 3.040 nonbonded pdb=" O THR H 111 " pdb=" OH TYR H 139 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 107 " pdb=" NZ LYS D 275 " model vdw 2.254 3.120 nonbonded pdb=" OG SER E 95 " pdb=" OD1 ASN F 88 " model vdw 2.255 3.040 nonbonded pdb=" O ASN G 5 " pdb=" OG SER G 8 " model vdw 2.276 3.040 ... (remaining 98613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 40 through 133) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.240 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.050 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.004 0.071 12231 Z= 0.240 Angle : 0.638 9.596 16808 Z= 0.478 Chirality : 0.040 0.161 1897 Planarity : 0.004 0.053 1854 Dihedral : 19.644 90.375 4900 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.42 % Allowed : 19.54 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.08 (0.23), residues: 1222 helix: 1.45 (0.19), residues: 740 sheet: 0.07 (0.76), residues: 47 loop : -0.40 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 265 TYR 0.008 0.001 TYR E 230 PHE 0.010 0.001 PHE H 177 TRP 0.015 0.001 TRP D 85 HIS 0.003 0.001 HIS E 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.24 (12231) covalent geometry : angle 0.63838 / 0.48 (16808) hydrogen bonds : bond 0.24592 / 16.27 ( 680) hydrogen bonds : angle 6.76182 / 4.81 ( 1892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 0.269 Fit side-chains REVERT: A 98 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: A 109 ASN cc_start: 0.7773 (t0) cc_final: 0.7200 (t0) REVERT: A 117 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7431 (mtm180) REVERT: A 124 ASP cc_start: 0.7903 (m-30) cc_final: 0.7662 (m-30) REVERT: B 63 LEU cc_start: 0.7628 (tp) cc_final: 0.7420 (tp) REVERT: C 49 LEU cc_start: 0.8131 (mt) cc_final: 0.7888 (mt) REVERT: C 50 ARG cc_start: 0.7235 (ttm170) cc_final: 0.6964 (tpp80) REVERT: D 16 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6837 (mt-10) REVERT: D 19 GLU cc_start: 0.6901 (tp30) cc_final: 0.6653 (tp30) REVERT: D 78 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6766 (p) REVERT: D 126 GLU cc_start: 0.7060 (tt0) cc_final: 0.6818 (tt0) REVERT: D 135 GLU cc_start: 0.6927 (tt0) cc_final: 0.6726 (tt0) REVERT: D 143 MET cc_start: 0.7399 (mtm) cc_final: 0.7146 (mtm) REVERT: D 162 LEU cc_start: 0.7930 (mt) cc_final: 0.7699 (mt) REVERT: D 169 LYS cc_start: 0.7945 (mttt) cc_final: 0.7593 (mttm) REVERT: D 183 GLU cc_start: 0.7613 (pt0) cc_final: 0.7297 (pm20) REVERT: D 277 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6803 (mt-10) REVERT: D 354 GLU cc_start: 0.7223 (tt0) cc_final: 0.6847 (tt0) REVERT: E 68 LEU cc_start: 0.7988 (mm) cc_final: 0.7784 (mt) REVERT: E 74 GLU cc_start: 0.6326 (tt0) cc_final: 0.6086 (tt0) REVERT: E 75 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7483 (tmtm) REVERT: E 80 GLU cc_start: 0.7659 (mp0) cc_final: 0.7459 (mp0) REVERT: E 94 THR cc_start: 0.7391 (p) cc_final: 0.7124 (m) REVERT: E 127 GLU cc_start: 0.7898 (tt0) cc_final: 0.7331 (tt0) REVERT: E 134 MET cc_start: 0.6615 (mtm) cc_final: 0.6387 (pp-130) REVERT: E 143 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6475 (mm-30) REVERT: E 181 LYS cc_start: 0.7278 (mttp) cc_final: 0.6956 (OUTLIER) REVERT: E 192 LYS cc_start: 0.7497 (tttt) cc_final: 0.6717 (tttp) REVERT: E 196 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6186 (mt-10) REVERT: E 198 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6444 (mm-30) REVERT: E 240 MET cc_start: 0.7815 (mtm) cc_final: 0.7574 (mtp) REVERT: E 241 ASN cc_start: 0.7596 (m110) cc_final: 0.7390 (m110) REVERT: E 261 LYS cc_start: 0.7560 (mmpt) cc_final: 0.7240 (mmtp) REVERT: E 271 LYS cc_start: 0.7487 (mmtp) cc_final: 0.7113 (mmtp) REVERT: E 273 ILE cc_start: 0.7962 (mm) cc_final: 0.7738 (mm) REVERT: E 275 LYS cc_start: 0.7533 (mmpt) cc_final: 0.7220 (mmpt) REVERT: E 276 LYS cc_start: 0.7505 (ttmm) cc_final: 0.7284 (ttmm) REVERT: E 293 LYS cc_start: 0.7500 (mtmt) cc_final: 0.7086 (mtmp) REVERT: E 302 GLU cc_start: 0.6546 (pp20) cc_final: 0.6132 (pp20) REVERT: E 317 LYS cc_start: 0.7584 (mttt) cc_final: 0.7287 (mtpt) REVERT: E 327 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6315 (mm-30) REVERT: E 341 TYR cc_start: 0.6529 (p90) cc_final: 0.5930 (p90) REVERT: F 77 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7557 (mm-40) REVERT: F 81 ASN cc_start: 0.7542 (m-40) cc_final: 0.7168 (m-40) REVERT: F 109 TYR cc_start: 0.8122 (m-80) cc_final: 0.7713 (m-80) REVERT: F 130 GLU cc_start: 0.6901 (mp0) cc_final: 0.6202 (mp0) REVERT: G 18 MET cc_start: 0.5063 (ptp) cc_final: 0.4658 (ptp) REVERT: G 78 LEU cc_start: 0.7574 (mt) cc_final: 0.7366 (mp) outliers start: 16 outliers final: 7 residues processed: 290 average time/residue: 0.6787 time to fit residues: 209.7058 Evaluate side-chains 261 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 253 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 181 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 248 GLN D 355 ASN D 356 GLN F 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130122 restraints weight = 14277.613| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.46 r_work: 0.3423 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12231 Z= 0.235 Angle : 0.685 11.379 16808 Z= 0.383 Chirality : 0.049 0.228 1897 Planarity : 0.005 0.043 1854 Dihedral : 19.995 66.326 2285 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.88 % Allowed : 19.80 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.46 (0.23), residues: 1222 helix: 1.86 (0.18), residues: 750 sheet: -0.57 (0.68), residues: 53 loop : -0.43 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 265 TYR 0.013 0.002 TYR E 230 PHE 0.018 0.002 PHE D 71 TRP 0.022 0.003 TRP D 85 HIS 0.006 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (12231) covalent geometry : angle 0.68482 / 0.38 (16808) hydrogen bonds : bond 0.06817 / 4.53 ( 680) hydrogen bonds : angle 4.71784 / 3.44 ( 1892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.414 Fit side-chains REVERT: A 97 VAL cc_start: 0.8560 (t) cc_final: 0.8333 (p) REVERT: A 98 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 109 ASN cc_start: 0.8528 (t0) cc_final: 0.8170 (t0) REVERT: A 124 ASP cc_start: 0.8133 (m-30) cc_final: 0.7757 (m-30) REVERT: C 64 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7995 (mtt90) REVERT: D 135 GLU cc_start: 0.7812 (tt0) cc_final: 0.7577 (tt0) REVERT: D 344 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: E 127 GLU cc_start: 0.8097 (tt0) cc_final: 0.7866 (tt0) REVERT: E 143 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7220 (mm-30) REVERT: E 187 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: E 192 LYS cc_start: 0.8446 (tttt) cc_final: 0.8203 (tttp) REVERT: E 200 ASP cc_start: 0.8045 (m-30) cc_final: 0.7844 (m-30) REVERT: E 293 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7500 (mtmp) REVERT: E 302 GLU cc_start: 0.7110 (pp20) cc_final: 0.6860 (pp20) REVERT: E 320 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7846 (ttt90) REVERT: E 341 TYR cc_start: 0.7218 (p90) cc_final: 0.6602 (p90) REVERT: F 130 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: G 18 MET cc_start: 0.6031 (ptp) cc_final: 0.5720 (ptp) REVERT: G 78 LEU cc_start: 0.8652 (mt) cc_final: 0.8434 (mp) REVERT: G 81 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7129 (tm-30) REVERT: H 103 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7539 (mm) REVERT: H 199 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5510 (pptt) outliers start: 55 outliers final: 22 residues processed: 279 average time/residue: 0.6459 time to fit residues: 191.9879 Evaluate side-chains 274 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 248 GLN D 356 GLN E 337 GLN F 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131269 restraints weight = 14313.413| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.46 r_work: 0.3436 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12231 Z= 0.211 Angle : 0.638 10.803 16808 Z= 0.355 Chirality : 0.047 0.222 1897 Planarity : 0.005 0.046 1854 Dihedral : 20.750 63.407 2277 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.60 % Allowed : 19.09 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.51 (0.23), residues: 1222 helix: 1.92 (0.18), residues: 743 sheet: -0.54 (0.64), residues: 68 loop : -0.40 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.014 0.002 TYR E 230 PHE 0.016 0.002 PHE F 90 TRP 0.021 0.003 TRP D 85 HIS 0.006 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (12231) covalent geometry : angle 0.63813 / 0.36 (16808) hydrogen bonds : bond 0.05888 / 3.88 ( 680) hydrogen bonds : angle 4.41033 / 3.23 ( 1892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.390 Fit side-chains REVERT: A 98 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 109 ASN cc_start: 0.8543 (t0) cc_final: 0.8182 (t0) REVERT: B 41 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7914 (mtt180) REVERT: D 344 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: E 127 GLU cc_start: 0.8094 (tt0) cc_final: 0.7850 (tt0) REVERT: E 143 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7123 (mm-30) REVERT: E 183 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: E 187 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7249 (pp20) REVERT: E 192 LYS cc_start: 0.8479 (tttt) cc_final: 0.8224 (tttp) REVERT: E 200 ASP cc_start: 0.8043 (m-30) cc_final: 0.7786 (m-30) REVERT: E 275 LYS cc_start: 0.8036 (mppt) cc_final: 0.7818 (mppt) REVERT: E 302 GLU cc_start: 0.7006 (pp20) cc_final: 0.6763 (pp20) REVERT: E 320 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7766 (ttt90) REVERT: E 341 TYR cc_start: 0.7270 (p90) cc_final: 0.6668 (p90) REVERT: F 77 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8078 (mm-40) REVERT: F 81 ASN cc_start: 0.8068 (m110) cc_final: 0.7798 (m110) REVERT: F 130 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: G 18 MET cc_start: 0.6020 (ptp) cc_final: 0.5772 (ptp) REVERT: G 81 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7263 (tm-30) outliers start: 63 outliers final: 27 residues processed: 268 average time/residue: 0.5811 time to fit residues: 166.3995 Evaluate side-chains 259 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 248 GLN D 294 HIS D 356 GLN E 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131830 restraints weight = 14225.843| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.46 r_work: 0.3446 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12231 Z= 0.208 Angle : 0.616 10.211 16808 Z= 0.343 Chirality : 0.046 0.211 1897 Planarity : 0.004 0.048 1854 Dihedral : 20.791 62.168 2276 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.53 % Allowed : 21.49 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.49 (0.23), residues: 1222 helix: 1.95 (0.18), residues: 743 sheet: -0.74 (0.64), residues: 63 loop : -0.46 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.014 0.002 TYR E 230 PHE 0.018 0.002 PHE F 90 TRP 0.021 0.003 TRP D 85 HIS 0.006 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (12231) covalent geometry : angle 0.61630 / 0.34 (16808) hydrogen bonds : bond 0.05516 / 3.66 ( 680) hydrogen bonds : angle 4.30337 / 3.14 ( 1892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.406 Fit side-chains REVERT: A 97 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 98 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 109 ASN cc_start: 0.8541 (t0) cc_final: 0.8152 (t160) REVERT: C 56 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: D 130 GLU cc_start: 0.7977 (mp0) cc_final: 0.7709 (mp0) REVERT: D 203 GLU cc_start: 0.7861 (tt0) cc_final: 0.7645 (tt0) REVERT: D 344 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: E 127 GLU cc_start: 0.8096 (tt0) cc_final: 0.7832 (tt0) REVERT: E 143 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 183 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: E 187 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: E 192 LYS cc_start: 0.8492 (tttt) cc_final: 0.8226 (tptp) REVERT: E 198 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7406 (mm-30) REVERT: E 275 LYS cc_start: 0.7982 (mppt) cc_final: 0.7748 (mppt) REVERT: E 302 GLU cc_start: 0.6983 (pp20) cc_final: 0.6736 (pp20) REVERT: E 320 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7761 (ttt90) REVERT: E 341 TYR cc_start: 0.7313 (p90) cc_final: 0.6707 (p90) REVERT: F 130 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: G 43 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: G 81 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7309 (tm-30) REVERT: H 91 ASN cc_start: 0.7611 (m-40) cc_final: 0.7325 (m110) outliers start: 51 outliers final: 26 residues processed: 263 average time/residue: 0.5964 time to fit residues: 167.5537 Evaluate side-chains 267 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 GLN D 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.162975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133225 restraints weight = 14225.425| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.46 r_work: 0.3469 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12231 Z= 0.157 Angle : 0.567 10.370 16808 Z= 0.317 Chirality : 0.042 0.205 1897 Planarity : 0.004 0.044 1854 Dihedral : 20.856 62.202 2276 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.97 % Allowed : 21.67 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.65 (0.23), residues: 1222 helix: 2.08 (0.18), residues: 743 sheet: -0.61 (0.66), residues: 63 loop : -0.42 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 64 TYR 0.012 0.001 TYR E 230 PHE 0.013 0.001 PHE F 90 TRP 0.018 0.002 TRP D 85 HIS 0.006 0.001 HIS E 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12231) covalent geometry : angle 0.56695 / 0.32 (16808) hydrogen bonds : bond 0.04937 / 3.28 ( 680) hydrogen bonds : angle 4.15187 / 3.03 ( 1892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8285 (p) REVERT: A 109 ASN cc_start: 0.8505 (t0) cc_final: 0.8150 (t160) REVERT: B 32 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (mttt) REVERT: C 41 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7813 (ttm110) REVERT: D 130 GLU cc_start: 0.7946 (mp0) cc_final: 0.7674 (mp0) REVERT: D 203 GLU cc_start: 0.7832 (tt0) cc_final: 0.7617 (tt0) REVERT: D 344 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: E 127 GLU cc_start: 0.8081 (tt0) cc_final: 0.7845 (tt0) REVERT: E 143 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7076 (mm-30) REVERT: E 187 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: E 192 LYS cc_start: 0.8488 (tttt) cc_final: 0.8231 (tptp) REVERT: E 198 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7352 (mm-30) REVERT: E 275 LYS cc_start: 0.7974 (mppt) cc_final: 0.7745 (mppt) REVERT: E 302 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6714 (pp20) REVERT: E 320 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7699 (ttt90) REVERT: E 341 TYR cc_start: 0.7318 (p90) cc_final: 0.6681 (p90) REVERT: F 130 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: G 81 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7263 (tm-30) REVERT: H 91 ASN cc_start: 0.7574 (m-40) cc_final: 0.7300 (m110) REVERT: H 160 ILE cc_start: 0.5040 (OUTLIER) cc_final: 0.4636 (pp) outliers start: 56 outliers final: 39 residues processed: 262 average time/residue: 0.6293 time to fit residues: 176.5791 Evaluate side-chains 277 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 356 GLN E 82 ASN E 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132378 restraints weight = 14219.994| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.47 r_work: 0.3453 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12231 Z= 0.200 Angle : 0.582 7.448 16808 Z= 0.325 Chirality : 0.044 0.192 1897 Planarity : 0.004 0.047 1854 Dihedral : 20.898 60.725 2276 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.97 % Allowed : 21.85 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.58 (0.23), residues: 1222 helix: 2.02 (0.18), residues: 743 sheet: -0.42 (0.66), residues: 68 loop : -0.47 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 64 TYR 0.015 0.002 TYR E 230 PHE 0.016 0.002 PHE F 90 TRP 0.019 0.003 TRP D 85 HIS 0.006 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (12231) covalent geometry : angle 0.58223 / 0.33 (16808) hydrogen bonds : bond 0.05272 / 3.50 ( 680) hydrogen bonds : angle 4.18669 / 3.06 ( 1892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8544 (t0) cc_final: 0.8179 (t160) REVERT: B 32 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (mttt) REVERT: C 41 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: C 49 LEU cc_start: 0.8715 (mp) cc_final: 0.8493 (mt) REVERT: D 105 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7889 (ttp-170) REVERT: D 130 GLU cc_start: 0.7963 (mp0) cc_final: 0.7707 (mp0) REVERT: D 203 GLU cc_start: 0.7833 (tt0) cc_final: 0.7624 (tt0) REVERT: D 344 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: E 127 GLU cc_start: 0.8097 (tt0) cc_final: 0.7872 (tt0) REVERT: E 143 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7115 (mm-30) REVERT: E 187 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7236 (pp20) REVERT: E 192 LYS cc_start: 0.8505 (tttt) cc_final: 0.8220 (tptp) REVERT: E 198 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7370 (mm-30) REVERT: E 275 LYS cc_start: 0.8002 (mppt) cc_final: 0.7760 (mppt) REVERT: E 302 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6696 (pp20) REVERT: E 341 TYR cc_start: 0.7338 (p90) cc_final: 0.6651 (p90) REVERT: F 74 TYR cc_start: 0.8583 (t80) cc_final: 0.8366 (t80) REVERT: F 130 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: G 81 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7302 (tm-30) REVERT: H 91 ASN cc_start: 0.7652 (m-40) cc_final: 0.7381 (m110) REVERT: H 160 ILE cc_start: 0.5025 (OUTLIER) cc_final: 0.4616 (pp) outliers start: 56 outliers final: 38 residues processed: 256 average time/residue: 0.5732 time to fit residues: 157.1538 Evaluate side-chains 274 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 356 GLN F 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132817 restraints weight = 14104.481| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.46 r_work: 0.3460 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12231 Z= 0.183 Angle : 0.572 7.435 16808 Z= 0.320 Chirality : 0.043 0.185 1897 Planarity : 0.004 0.047 1854 Dihedral : 20.910 60.095 2276 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.42 % Allowed : 21.05 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.62 (0.23), residues: 1222 helix: 2.06 (0.18), residues: 742 sheet: -0.34 (0.68), residues: 68 loop : -0.46 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 117 TYR 0.014 0.001 TYR E 230 PHE 0.015 0.002 PHE F 90 TRP 0.019 0.002 TRP D 85 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (12231) covalent geometry : angle 0.57158 / 0.32 (16808) hydrogen bonds : bond 0.05089 / 3.37 ( 680) hydrogen bonds : angle 4.15387 / 3.04 ( 1892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8528 (t0) cc_final: 0.8175 (t160) REVERT: A 132 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7004 (mtp85) REVERT: B 32 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8296 (mttt) REVERT: C 41 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7857 (ttm110) REVERT: C 49 LEU cc_start: 0.8719 (mp) cc_final: 0.8492 (mt) REVERT: D 105 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7891 (ttp-170) REVERT: D 130 GLU cc_start: 0.7954 (mp0) cc_final: 0.7699 (mp0) REVERT: D 203 GLU cc_start: 0.7833 (tt0) cc_final: 0.7628 (tt0) REVERT: D 344 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: E 127 GLU cc_start: 0.8107 (tt0) cc_final: 0.7877 (tt0) REVERT: E 143 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7118 (mm-30) REVERT: E 187 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: E 192 LYS cc_start: 0.8507 (tttt) cc_final: 0.8244 (tptp) REVERT: E 198 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7371 (mm-30) REVERT: E 275 LYS cc_start: 0.8019 (mppt) cc_final: 0.7770 (mppt) REVERT: E 302 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6695 (pp20) REVERT: E 341 TYR cc_start: 0.7339 (p90) cc_final: 0.6658 (p90) REVERT: F 130 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: G 81 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7308 (tm-30) REVERT: H 91 ASN cc_start: 0.7676 (m-40) cc_final: 0.7399 (m110) REVERT: H 160 ILE cc_start: 0.4994 (OUTLIER) cc_final: 0.4574 (pp) outliers start: 61 outliers final: 43 residues processed: 260 average time/residue: 0.5800 time to fit residues: 161.3831 Evaluate side-chains 282 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 66 optimal weight: 0.0020 chunk 123 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 356 GLN H 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134121 restraints weight = 14179.736| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.46 r_work: 0.3478 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12231 Z= 0.150 Angle : 0.550 7.524 16808 Z= 0.308 Chirality : 0.041 0.174 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.933 60.118 2276 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.97 % Allowed : 22.02 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.76 (0.24), residues: 1222 helix: 2.17 (0.18), residues: 742 sheet: -0.27 (0.68), residues: 68 loop : -0.43 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 64 TYR 0.013 0.001 TYR E 230 PHE 0.012 0.001 PHE F 90 TRP 0.017 0.002 TRP D 85 HIS 0.005 0.001 HIS E 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (12231) covalent geometry : angle 0.55006 / 0.31 (16808) hydrogen bonds : bond 0.04717 / 3.13 ( 680) hydrogen bonds : angle 4.06548 / 2.98 ( 1892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8485 (t0) cc_final: 0.8130 (t160) REVERT: A 132 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6966 (mtp85) REVERT: B 32 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (mttt) REVERT: C 41 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7847 (ttm110) REVERT: D 105 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7883 (ttp-170) REVERT: D 344 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: E 127 GLU cc_start: 0.8107 (tt0) cc_final: 0.7885 (tt0) REVERT: E 143 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7096 (mm-30) REVERT: E 187 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: E 192 LYS cc_start: 0.8497 (tttt) cc_final: 0.8245 (tptp) REVERT: E 198 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7371 (mm-30) REVERT: E 275 LYS cc_start: 0.8013 (mppt) cc_final: 0.7783 (mppt) REVERT: E 302 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6683 (pp20) REVERT: E 341 TYR cc_start: 0.7321 (p90) cc_final: 0.6620 (p90) REVERT: F 130 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: G 81 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7314 (tm-30) REVERT: H 91 ASN cc_start: 0.7647 (m-40) cc_final: 0.7364 (m110) REVERT: H 160 ILE cc_start: 0.4958 (OUTLIER) cc_final: 0.4551 (pp) outliers start: 56 outliers final: 41 residues processed: 253 average time/residue: 0.5618 time to fit residues: 152.1395 Evaluate side-chains 273 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 356 GLN F 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.164070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134417 restraints weight = 14146.472| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.46 r_work: 0.3483 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12231 Z= 0.142 Angle : 0.545 7.289 16808 Z= 0.304 Chirality : 0.041 0.165 1897 Planarity : 0.004 0.042 1854 Dihedral : 20.943 59.997 2276 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.15 % Allowed : 21.85 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.82 (0.24), residues: 1222 helix: 2.23 (0.19), residues: 743 sheet: -0.34 (0.67), residues: 68 loop : -0.42 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 117 TYR 0.012 0.001 TYR E 230 PHE 0.012 0.001 PHE D 70 TRP 0.017 0.002 TRP E 148 HIS 0.004 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12231) covalent geometry : angle 0.54539 / 0.30 (16808) hydrogen bonds : bond 0.04604 / 3.06 ( 680) hydrogen bonds : angle 4.02367 / 2.95 ( 1892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8473 (t0) cc_final: 0.8124 (t160) REVERT: A 132 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.6962 (mtp85) REVERT: B 32 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8270 (mttt) REVERT: C 41 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7871 (ttm110) REVERT: D 105 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7878 (ttp-170) REVERT: D 130 GLU cc_start: 0.7922 (mp0) cc_final: 0.7630 (mp0) REVERT: D 344 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: E 127 GLU cc_start: 0.8109 (tt0) cc_final: 0.7888 (tt0) REVERT: E 143 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7104 (mm-30) REVERT: E 183 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: E 187 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: E 192 LYS cc_start: 0.8476 (tttt) cc_final: 0.8243 (tptp) REVERT: E 198 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7331 (mm-30) REVERT: E 275 LYS cc_start: 0.8012 (mppt) cc_final: 0.7774 (mppt) REVERT: E 302 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: E 341 TYR cc_start: 0.7309 (p90) cc_final: 0.6572 (p90) REVERT: F 130 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: G 38 ILE cc_start: 0.8232 (pt) cc_final: 0.7922 (mt) REVERT: G 81 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7305 (tm-30) REVERT: H 91 ASN cc_start: 0.7639 (m-40) cc_final: 0.7370 (m110) REVERT: H 160 ILE cc_start: 0.4908 (OUTLIER) cc_final: 0.4513 (pp) outliers start: 58 outliers final: 44 residues processed: 255 average time/residue: 0.6053 time to fit residues: 165.1348 Evaluate side-chains 280 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 0.0020 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN D 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134608 restraints weight = 14134.756| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.47 r_work: 0.3485 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12231 Z= 0.144 Angle : 0.545 7.118 16808 Z= 0.304 Chirality : 0.041 0.165 1897 Planarity : 0.004 0.058 1854 Dihedral : 20.941 59.899 2276 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.06 % Allowed : 22.20 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.81 (0.24), residues: 1222 helix: 2.23 (0.19), residues: 743 sheet: -0.32 (0.67), residues: 68 loop : -0.43 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 117 TYR 0.013 0.001 TYR E 230 PHE 0.013 0.001 PHE D 70 TRP 0.016 0.002 TRP D 85 HIS 0.004 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12231) covalent geometry : angle 0.54529 / 0.30 (16808) hydrogen bonds : bond 0.04580 / 3.05 ( 680) hydrogen bonds : angle 4.01529 / 2.93 ( 1892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8468 (t0) cc_final: 0.8120 (t160) REVERT: A 132 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6946 (mtp85) REVERT: B 32 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (mttt) REVERT: C 41 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: D 105 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: D 344 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: E 127 GLU cc_start: 0.8072 (tt0) cc_final: 0.7854 (tt0) REVERT: E 143 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7078 (mm-30) REVERT: E 183 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: E 187 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7103 (pp20) REVERT: E 192 LYS cc_start: 0.8477 (tttt) cc_final: 0.8241 (tptp) REVERT: E 198 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7273 (mm-30) REVERT: E 275 LYS cc_start: 0.8007 (mppt) cc_final: 0.7763 (mppt) REVERT: E 302 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: E 341 TYR cc_start: 0.7317 (p90) cc_final: 0.6537 (p90) REVERT: F 130 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: G 38 ILE cc_start: 0.8176 (pt) cc_final: 0.7854 (mt) REVERT: G 81 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7292 (tm-30) REVERT: H 91 ASN cc_start: 0.7640 (m-40) cc_final: 0.7373 (m110) REVERT: H 160 ILE cc_start: 0.4888 (OUTLIER) cc_final: 0.4502 (pp) outliers start: 57 outliers final: 44 residues processed: 257 average time/residue: 0.6167 time to fit residues: 169.5485 Evaluate side-chains 279 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133493 restraints weight = 14178.355| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.46 r_work: 0.3467 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12231 Z= 0.186 Angle : 0.574 7.181 16808 Z= 0.319 Chirality : 0.043 0.253 1897 Planarity : 0.004 0.046 1854 Dihedral : 20.922 59.791 2276 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.06 % Allowed : 22.38 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.69 (0.23), residues: 1222 helix: 2.16 (0.18), residues: 736 sheet: -0.39 (0.66), residues: 68 loop : -0.50 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.014 0.002 TYR E 230 PHE 0.017 0.002 PHE D 70 TRP 0.019 0.003 TRP D 85 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (12231) covalent geometry : angle 0.57394 / 0.32 (16808) hydrogen bonds : bond 0.04981 / 3.31 ( 680) hydrogen bonds : angle 4.06486 / 2.97 ( 1892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4628.48 seconds wall clock time: 79 minutes 24.34 seconds (4764.34 seconds total)