Starting phenix.real_space_refine on Fri Sep 11 21:28:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0o_14428/09_2026/7z0o_14428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0o_14428/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z0o_14428/09_2026/7z0o_14428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0o_14428/09_2026/7z0o_14428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z0o_14428/09_2026/7z0o_14428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0o_14428/09_2026/7z0o_14428.map" } 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-2.2.1-6174/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: 2.54, per 1000 atoms: 0.21 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: 0.85 Conformation dependent library (CDL) restraints added in 441.3 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: 1.37 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: 2.16 Time building geometry restraints manager: 1.19 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: 6.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- 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 : 0.640 9.596 16808 Z= 0.479 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 0.63965 / 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 : 0.465 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: 0.7808 (mt) REVERT: C 50 ARG cc_start: 0.7235 (ttm170) cc_final: 0.6960 (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: 0.7250 time to fit residues: 223.8626 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 : 0.414 ------------------------------------------------------------------------------- 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: 0.6980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.160412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130646 restraints weight = 14264.426| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.46 r_work: 0.3433 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12231 Z= 0.222 Angle : 0.696 11.403 16808 Z= 0.384 Chirality : 0.049 0.238 1897 Planarity : 0.005 0.044 1854 Dihedral : 20.092 65.681 2285 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.88 % Allowed : 19.45 % Favored : 75.67 % 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: 1.41 (0.23), residues: 1222 helix: 1.81 (0.18), residues: 748 sheet: -0.60 (0.67), residues: 53 loop : -0.40 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 265 TYR 0.012 0.002 TYR F 73 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 0.00496 / 0.22 (12231) covalent geometry : angle 0.69595 / 0.38 (16808) hydrogen bonds : bond 0.06762 / 4.48 ( 680) hydrogen bonds : angle 4.64811 / 3.39 ( 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 310 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 0.422 Fit side-chains REVERT: A 97 VAL cc_start: 0.8562 (t) cc_final: 0.8336 (p) REVERT: A 98 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: A 109 ASN cc_start: 0.8516 (t0) cc_final: 0.8137 (t160) REVERT: A 117 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7914 (mtm180) REVERT: A 124 ASP cc_start: 0.8115 (m-30) cc_final: 0.7792 (m-30) REVERT: C 64 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7985 (mtt90) REVERT: D 135 GLU cc_start: 0.7781 (tt0) cc_final: 0.7538 (tt0) REVERT: D 285 LYS cc_start: 0.8052 (pttt) cc_final: 0.7852 (pttt) REVERT: D 344 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: E 127 GLU cc_start: 0.8098 (tt0) cc_final: 0.7877 (tt0) REVERT: E 143 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7211 (mm-30) REVERT: E 187 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7400 (pp20) REVERT: E 192 LYS cc_start: 0.8464 (tttt) cc_final: 0.8226 (tttp) REVERT: E 200 ASP cc_start: 0.8069 (m-30) cc_final: 0.7868 (m-30) REVERT: E 275 LYS cc_start: 0.7924 (mmpt) cc_final: 0.7694 (mmpt) REVERT: E 293 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7418 (mtmm) REVERT: E 302 GLU cc_start: 0.7104 (pp20) cc_final: 0.6859 (pp20) REVERT: E 320 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7833 (ttt90) REVERT: E 341 TYR cc_start: 0.7208 (p90) cc_final: 0.6598 (p90) REVERT: F 130 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: G 18 MET cc_start: 0.6022 (ptp) cc_final: 0.5718 (ptp) REVERT: G 78 LEU cc_start: 0.8658 (mt) cc_final: 0.8447 (mp) REVERT: G 81 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7149 (tm-30) REVERT: H 103 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7552 (mm) REVERT: H 199 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5511 (pptt) outliers start: 55 outliers final: 24 residues processed: 283 average time/residue: 0.7011 time to fit residues: 211.9031 Evaluate side-chains 279 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 194 LEU 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 Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 248 GLN D 294 HIS D 355 ASN D 356 GLN E 337 GLN F 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132062 restraints weight = 14363.380| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.46 r_work: 0.3447 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12231 Z= 0.166 Angle : 0.603 10.682 16808 Z= 0.338 Chirality : 0.044 0.221 1897 Planarity : 0.004 0.042 1854 Dihedral : 20.516 63.472 2277 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.80 % Allowed : 20.16 % Favored : 75.04 % 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: 1.67 (0.23), residues: 1222 helix: 2.05 (0.18), residues: 749 sheet: -0.66 (0.63), residues: 63 loop : -0.33 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 129 TYR 0.012 0.001 TYR E 230 PHE 0.013 0.002 PHE F 90 TRP 0.018 0.002 TRP D 85 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (12231) covalent geometry : angle 0.60264 / 0.34 (16808) hydrogen bonds : bond 0.05590 / 3.70 ( 680) hydrogen bonds : angle 4.34425 / 3.18 ( 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 287 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.413 Fit side-chains REVERT: A 98 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 109 ASN cc_start: 0.8514 (t0) cc_final: 0.8134 (t0) REVERT: A 117 ARG cc_start: 0.8153 (mtm110) cc_final: 0.7897 (mtm180) REVERT: B 41 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7943 (mtt180) REVERT: D 344 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: E 127 GLU cc_start: 0.8086 (tt0) cc_final: 0.7840 (tt0) REVERT: E 143 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7125 (mm-30) REVERT: E 187 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7292 (pp20) REVERT: E 192 LYS cc_start: 0.8470 (tttt) cc_final: 0.8199 (tttp) REVERT: E 200 ASP cc_start: 0.8054 (m-30) cc_final: 0.7802 (m-30) REVERT: E 275 LYS cc_start: 0.7921 (mmpt) cc_final: 0.7638 (mmpt) REVERT: E 302 GLU cc_start: 0.7048 (pp20) cc_final: 0.6785 (pp20) REVERT: E 320 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7783 (ttt90) REVERT: E 341 TYR cc_start: 0.7252 (p90) cc_final: 0.6655 (p90) REVERT: F 130 GLU cc_start: 0.7602 (mp0) cc_final: 0.7122 (mp0) REVERT: G 81 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 54 outliers final: 27 residues processed: 263 average time/residue: 0.6909 time to fit residues: 194.1725 Evaluate side-chains 261 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 98 GLU Chi-restraints excluded: chain B residue 41 ARG 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 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 65 GLU 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 194 LEU 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 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 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 57 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 248 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132247 restraints weight = 14263.506| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.46 r_work: 0.3456 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12231 Z= 0.178 Angle : 0.592 10.017 16808 Z= 0.329 Chirality : 0.044 0.216 1897 Planarity : 0.004 0.045 1854 Dihedral : 20.678 61.660 2276 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.53 % Allowed : 20.25 % Favored : 75.22 % 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: 1.66 (0.23), residues: 1222 helix: 2.07 (0.18), residues: 749 sheet: -0.72 (0.63), residues: 63 loop : -0.39 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 64 TYR 0.012 0.001 TYR E 230 PHE 0.015 0.002 PHE F 90 TRP 0.018 0.002 TRP D 85 HIS 0.006 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (12231) covalent geometry : angle 0.59236 / 0.33 (16808) hydrogen bonds : bond 0.05300 / 3.51 ( 680) hydrogen bonds : angle 4.22265 / 3.08 ( 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 278 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.412 Fit side-chains REVERT: A 98 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: A 109 ASN cc_start: 0.8513 (t0) cc_final: 0.8149 (t160) REVERT: A 117 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7856 (mtm180) REVERT: D 135 GLU cc_start: 0.7798 (tt0) cc_final: 0.7383 (tt0) REVERT: D 203 GLU cc_start: 0.7857 (tt0) cc_final: 0.7651 (tt0) REVERT: D 344 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: E 127 GLU cc_start: 0.8082 (tt0) cc_final: 0.7823 (tt0) REVERT: E 143 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7091 (mm-30) REVERT: E 187 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: E 192 LYS cc_start: 0.8487 (tttt) cc_final: 0.8212 (tttp) REVERT: E 198 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7459 (mm-30) REVERT: E 200 ASP cc_start: 0.8050 (m-30) cc_final: 0.7785 (m-30) REVERT: E 275 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7650 (mmpt) REVERT: E 302 GLU cc_start: 0.7033 (pp20) cc_final: 0.6792 (pp20) REVERT: E 320 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7773 (ttt90) REVERT: E 341 TYR cc_start: 0.7289 (p90) cc_final: 0.6653 (p90) REVERT: F 130 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: G 81 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 51 outliers final: 35 residues processed: 256 average time/residue: 0.6967 time to fit residues: 190.1972 Evaluate side-chains 263 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 60 LYS Chi-restraints excluded: chain C residue 51 GLU 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 65 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 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 4 LEU Chi-restraints excluded: chain G residue 57 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 248 GLN D 356 GLN E 82 ASN E 337 GLN F 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133512 restraints weight = 14220.445| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.46 r_work: 0.3473 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12231 Z= 0.155 Angle : 0.568 9.852 16808 Z= 0.316 Chirality : 0.043 0.205 1897 Planarity : 0.004 0.042 1854 Dihedral : 20.758 61.335 2276 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.35 % Allowed : 21.23 % Favored : 74.42 % 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: 1.78 (0.23), residues: 1222 helix: 2.19 (0.18), residues: 743 sheet: -0.61 (0.65), residues: 63 loop : -0.37 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 64 TYR 0.011 0.001 TYR E 230 PHE 0.013 0.001 PHE F 90 TRP 0.017 0.002 TRP D 85 HIS 0.007 0.001 HIS E 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (12231) covalent geometry : angle 0.56785 / 0.32 (16808) hydrogen bonds : bond 0.04913 / 3.26 ( 680) hydrogen bonds : angle 4.11987 / 3.01 ( 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 280 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.288 Fit side-chains REVERT: A 98 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 109 ASN cc_start: 0.8486 (t0) cc_final: 0.8140 (t160) REVERT: A 117 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7853 (mtm180) REVERT: B 41 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7887 (mtt180) REVERT: D 135 GLU cc_start: 0.7777 (tt0) cc_final: 0.7298 (tt0) REVERT: D 203 GLU cc_start: 0.7829 (tt0) cc_final: 0.7620 (tt0) REVERT: D 344 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: E 127 GLU cc_start: 0.8073 (tt0) cc_final: 0.7816 (tt0) REVERT: E 143 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7058 (mm-30) REVERT: E 187 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: E 192 LYS cc_start: 0.8469 (tttt) cc_final: 0.8229 (tptp) REVERT: E 198 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7396 (mm-30) REVERT: E 275 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7626 (mmpt) REVERT: E 302 GLU cc_start: 0.7025 (pp20) cc_final: 0.6766 (pp20) REVERT: E 320 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7731 (ttt90) REVERT: E 341 TYR cc_start: 0.7304 (p90) cc_final: 0.6620 (p90) REVERT: F 130 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: G 81 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7297 (tm-30) REVERT: H 160 ILE cc_start: 0.4975 (OUTLIER) cc_final: 0.4570 (pp) outliers start: 49 outliers final: 34 residues processed: 258 average time/residue: 0.6891 time to fit residues: 190.1551 Evaluate side-chains 266 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 A residue 110 LEU 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 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 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 25 THR Chi-restraints excluded: chain G residue 57 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 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 356 GLN E 337 GLN F 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130581 restraints weight = 14206.498| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.46 r_work: 0.3426 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 12231 Z= 0.298 Angle : 0.674 10.578 16808 Z= 0.371 Chirality : 0.050 0.185 1897 Planarity : 0.005 0.053 1854 Dihedral : 20.871 60.737 2276 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.06 % Allowed : 21.40 % 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: 1.23 (0.23), residues: 1222 helix: 1.72 (0.18), residues: 742 sheet: -0.56 (0.65), residues: 68 loop : -0.56 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 64 TYR 0.022 0.002 TYR F 74 PHE 0.023 0.003 PHE F 90 TRP 0.025 0.004 TRP D 85 HIS 0.009 0.002 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.30 (12231) covalent geometry : angle 0.67411 / 0.37 (16808) hydrogen bonds : bond 0.06264 / 4.15 ( 680) hydrogen bonds : angle 4.41289 / 3.21 ( 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 296 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 0.372 Fit side-chains REVERT: A 98 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 109 ASN cc_start: 0.8569 (t0) cc_final: 0.8204 (t160) REVERT: B 32 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8416 (mmtt) REVERT: C 49 LEU cc_start: 0.8695 (mp) cc_final: 0.8468 (mt) REVERT: C 56 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: D 105 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7859 (ttp-170) REVERT: D 135 GLU cc_start: 0.7860 (tt0) cc_final: 0.7403 (tt0) REVERT: D 203 GLU cc_start: 0.7824 (tt0) cc_final: 0.7616 (tt0) REVERT: D 344 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: E 127 GLU cc_start: 0.8071 (tt0) cc_final: 0.7802 (tt0) REVERT: E 143 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7114 (mm-30) REVERT: E 183 ASP cc_start: 0.7893 (m-30) cc_final: 0.7590 (m-30) REVERT: E 187 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: E 192 LYS cc_start: 0.8462 (tttt) cc_final: 0.8188 (tptp) REVERT: E 198 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7328 (mm-30) REVERT: E 275 LYS cc_start: 0.7929 (mmpt) cc_final: 0.7662 (mmpt) REVERT: E 302 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6709 (pp20) REVERT: E 320 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7761 (ttt90) REVERT: E 341 TYR cc_start: 0.7369 (p90) cc_final: 0.6703 (p90) REVERT: F 130 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: G 50 LEU cc_start: 0.7602 (mp) cc_final: 0.7254 (mp) REVERT: G 78 LEU cc_start: 0.8655 (mt) cc_final: 0.8422 (mp) REVERT: G 81 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7328 (tm-30) outliers start: 57 outliers final: 35 residues processed: 265 average time/residue: 0.6911 time to fit residues: 195.8381 Evaluate side-chains 278 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 A residue 110 LEU 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 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 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 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 E residue 320 ARG 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 57 LEU 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 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: 0.6980 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 356 GLN F 61 ASN F 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132764 restraints weight = 14092.483| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.46 r_work: 0.3457 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12231 Z= 0.173 Angle : 0.594 10.255 16808 Z= 0.328 Chirality : 0.044 0.189 1897 Planarity : 0.004 0.047 1854 Dihedral : 20.846 59.975 2276 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.53 % Allowed : 22.02 % Favored : 73.45 % 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: 1.50 (0.23), residues: 1222 helix: 1.98 (0.18), residues: 742 sheet: -0.61 (0.65), residues: 63 loop : -0.52 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 64 TYR 0.013 0.001 TYR E 230 PHE 0.016 0.002 PHE F 90 TRP 0.020 0.003 TRP D 85 HIS 0.007 0.001 HIS E 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (12231) covalent geometry : angle 0.59383 / 0.33 (16808) hydrogen bonds : bond 0.05217 / 3.46 ( 680) hydrogen bonds : angle 4.23455 / 3.09 ( 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 282 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.362 Fit side-chains REVERT: A 98 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 109 ASN cc_start: 0.8517 (t0) cc_final: 0.8125 (t160) REVERT: C 49 LEU cc_start: 0.8700 (mp) cc_final: 0.8471 (mt) REVERT: C 56 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: D 135 GLU cc_start: 0.7818 (tt0) cc_final: 0.7373 (tt0) REVERT: D 203 GLU cc_start: 0.7822 (tt0) cc_final: 0.7610 (tt0) REVERT: D 344 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: E 127 GLU cc_start: 0.8100 (tt0) cc_final: 0.7873 (tt0) REVERT: E 143 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7122 (mm-30) REVERT: E 187 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: E 192 LYS cc_start: 0.8492 (tttt) cc_final: 0.8217 (tptp) REVERT: E 198 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7324 (mm-30) REVERT: E 275 LYS cc_start: 0.7931 (mmpt) cc_final: 0.7655 (mmpt) REVERT: E 302 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6707 (pp20) REVERT: E 320 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7731 (ttt90) REVERT: E 341 TYR cc_start: 0.7342 (p90) cc_final: 0.6687 (p90) REVERT: F 74 TYR cc_start: 0.8485 (t80) cc_final: 0.8239 (t80) REVERT: F 130 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: G 81 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7294 (tm-30) REVERT: H 91 ASN cc_start: 0.7650 (m-40) cc_final: 0.7384 (m110) REVERT: H 160 ILE cc_start: 0.5049 (OUTLIER) cc_final: 0.4631 (pp) outliers start: 51 outliers final: 36 residues processed: 254 average time/residue: 0.6862 time to fit residues: 186.3206 Evaluate side-chains 276 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 56 GLN 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 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 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 227 LYS 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 4 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 57 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 199 LYS 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: 0.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 66 optimal weight: 0.0050 chunk 123 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 356 GLN E 337 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 = 0.3994 r_free = 0.3994 target = 0.162906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132976 restraints weight = 14165.588| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.46 r_work: 0.3459 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2710 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= 0.174 Angle : 0.579 10.117 16808 Z= 0.321 Chirality : 0.043 0.177 1897 Planarity : 0.004 0.046 1854 Dihedral : 20.896 59.950 2276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.80 % Allowed : 21.67 % 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: 1.58 (0.23), residues: 1222 helix: 2.05 (0.18), residues: 742 sheet: -0.38 (0.66), residues: 68 loop : -0.54 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 64 TYR 0.013 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 0.00382 / 0.17 (12231) covalent geometry : angle 0.57938 / 0.32 (16808) hydrogen bonds : bond 0.05046 / 3.35 ( 680) hydrogen bonds : angle 4.17502 / 3.05 ( 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 286 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8500 (t0) cc_final: 0.8129 (t160) REVERT: A 132 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6989 (mtp85) REVERT: C 49 LEU cc_start: 0.8706 (mp) cc_final: 0.8491 (mt) REVERT: C 56 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: D 135 GLU cc_start: 0.7802 (tt0) cc_final: 0.7385 (tt0) REVERT: D 203 GLU cc_start: 0.7832 (tt0) cc_final: 0.7625 (tt0) REVERT: D 344 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: E 127 GLU cc_start: 0.8127 (tt0) cc_final: 0.7894 (tt0) REVERT: E 143 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7093 (mm-30) REVERT: E 187 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7178 (pp20) REVERT: E 192 LYS cc_start: 0.8502 (tttt) cc_final: 0.8233 (tptp) REVERT: E 198 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 275 LYS cc_start: 0.7937 (mmpt) cc_final: 0.7667 (mmpt) REVERT: E 302 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6689 (pp20) REVERT: E 320 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7742 (ttt90) REVERT: E 341 TYR cc_start: 0.7352 (p90) cc_final: 0.6664 (p90) REVERT: F 130 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: G 81 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7298 (tm-30) REVERT: H 91 ASN cc_start: 0.7662 (m-40) cc_final: 0.7391 (m110) REVERT: H 160 ILE cc_start: 0.5060 (OUTLIER) cc_final: 0.4657 (pp) outliers start: 54 outliers final: 40 residues processed: 259 average time/residue: 0.6753 time to fit residues: 187.0198 Evaluate side-chains 278 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 A residue 132 ARG 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 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 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 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 E residue 320 ARG 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 57 LEU Chi-restraints excluded: chain H residue 68 GLN 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 223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.163710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133691 restraints weight = 14144.923| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.46 r_work: 0.3474 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12231 Z= 0.156 Angle : 0.576 10.039 16808 Z= 0.318 Chirality : 0.042 0.171 1897 Planarity : 0.004 0.044 1854 Dihedral : 20.895 59.948 2276 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.53 % Allowed : 22.56 % Favored : 72.91 % 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: 2.11 (0.18), residues: 742 sheet: -0.50 (0.67), residues: 63 loop : -0.50 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.013 0.001 TYR E 230 PHE 0.013 0.001 PHE D 70 TRP 0.018 0.002 TRP D 85 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12231) covalent geometry : angle 0.57639 / 0.32 (16808) hydrogen bonds : bond 0.04853 / 3.22 ( 680) hydrogen bonds : angle 4.13325 / 3.02 ( 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 282 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8471 (t0) cc_final: 0.8097 (t160) REVERT: A 132 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.6979 (mtp85) REVERT: C 49 LEU cc_start: 0.8704 (mp) cc_final: 0.8486 (mt) REVERT: D 135 GLU cc_start: 0.7793 (tt0) cc_final: 0.7372 (tt0) REVERT: D 203 GLU cc_start: 0.7825 (tt0) cc_final: 0.7622 (tt0) REVERT: D 344 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: E 127 GLU cc_start: 0.8132 (tt0) cc_final: 0.7900 (tt0) REVERT: E 143 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7104 (mm-30) REVERT: E 187 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: E 192 LYS cc_start: 0.8511 (tttt) cc_final: 0.8247 (tptp) REVERT: E 198 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7304 (mm-30) REVERT: E 275 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7661 (mmpt) REVERT: E 302 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: E 341 TYR cc_start: 0.7347 (p90) cc_final: 0.6619 (p90) REVERT: F 130 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: G 81 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7295 (tm-30) REVERT: H 91 ASN cc_start: 0.7671 (m-40) cc_final: 0.7414 (m110) REVERT: H 160 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4602 (pp) outliers start: 51 outliers final: 40 residues processed: 257 average time/residue: 0.6607 time to fit residues: 182.1418 Evaluate side-chains 278 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 A residue 132 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 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 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 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 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 57 LEU 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 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 93 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.163666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133636 restraints weight = 14214.829| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.46 r_work: 0.3475 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12231 Z= 0.165 Angle : 0.580 10.088 16808 Z= 0.319 Chirality : 0.042 0.167 1897 Planarity : 0.004 0.044 1854 Dihedral : 20.899 59.883 2276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.53 % Allowed : 22.56 % Favored : 72.91 % 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: 2.11 (0.18), residues: 742 sheet: -0.48 (0.68), residues: 63 loop : -0.49 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.013 0.001 TYR E 230 PHE 0.015 0.002 PHE D 70 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 0.00359 / 0.16 (12231) covalent geometry : angle 0.57971 / 0.32 (16808) hydrogen bonds : bond 0.04875 / 3.23 ( 680) hydrogen bonds : angle 4.11595 / 3.01 ( 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: 51 poor density : 236 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8489 (t0) cc_final: 0.8134 (t160) REVERT: A 132 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6994 (mtp85) REVERT: B 32 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8368 (mmtt) REVERT: C 49 LEU cc_start: 0.8706 (mp) cc_final: 0.8487 (mt) REVERT: C 56 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: D 135 GLU cc_start: 0.7793 (tt0) cc_final: 0.7369 (tt0) REVERT: D 203 GLU cc_start: 0.7822 (tt0) cc_final: 0.7620 (tt0) REVERT: D 344 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: E 127 GLU cc_start: 0.8121 (tt0) cc_final: 0.7890 (tt0) REVERT: E 143 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 183 ASP cc_start: 0.7806 (m-30) cc_final: 0.7581 (m-30) REVERT: E 187 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: E 192 LYS cc_start: 0.8509 (tttt) cc_final: 0.8251 (tptp) REVERT: E 198 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7325 (mm-30) REVERT: E 275 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7678 (mmpt) REVERT: E 302 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: E 341 TYR cc_start: 0.7351 (p90) cc_final: 0.6645 (p90) REVERT: F 130 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: G 38 ILE cc_start: 0.8239 (pt) cc_final: 0.7921 (mt) REVERT: G 81 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7305 (tm-30) REVERT: H 91 ASN cc_start: 0.7692 (m-40) cc_final: 0.7442 (m110) REVERT: H 160 ILE cc_start: 0.4917 (OUTLIER) cc_final: 0.4543 (pp) outliers start: 51 outliers final: 39 residues processed: 263 average time/residue: 0.6554 time to fit residues: 184.6999 Evaluate side-chains 280 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 A residue 132 ARG 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 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 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 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 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 57 LEU 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 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.0570 chunk 90 optimal weight: 0.0970 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN C 121 GLN D 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134636 restraints weight = 14191.565| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.46 r_work: 0.3487 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12231 Z= 0.142 Angle : 0.561 9.965 16808 Z= 0.309 Chirality : 0.041 0.162 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.893 59.963 2276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.17 % Allowed : 22.91 % Favored : 72.91 % 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: 1.78 (0.24), residues: 1222 helix: 2.22 (0.19), residues: 742 sheet: -0.46 (0.68), residues: 63 loop : -0.44 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.013 0.001 TYR E 230 PHE 0.011 0.001 PHE D 70 TRP 0.018 0.002 TRP D 85 HIS 0.004 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (12231) covalent geometry : angle 0.56090 / 0.31 (16808) hydrogen bonds : bond 0.04605 / 3.05 ( 680) hydrogen bonds : angle 4.04819 / 2.96 ( 1892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5114.30 seconds wall clock time: 87 minutes 42.46 seconds (5262.46 seconds total)