Starting phenix.real_space_refine on Wed Mar 4 16:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.map" model { file = "/net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ouh_13077/03_2026/7ouh_13077.cif" } resolution = 3.5 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= 0.024 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9426 2.51 5 N 2704 2.21 5 O 2822 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15088 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 103.581 121.200 24.861 1.00 69.67 S ATOM 260 SG CYS D 38 101.163 123.339 26.815 1.00 63.60 S ATOM 2296 SG CYS E 35 72.912 56.350 37.343 1.00 19.02 S ATOM 2317 SG CYS E 38 70.277 57.163 37.546 1.00 18.08 S Restraints were copied for chains: A, B, C, K, L Time building chain proxies: 4.13, per 1000 atoms: 0.27 Number of scatterers: 15088 At special positions: 0 Unit cell: (126.5, 166.1, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 6 9.00 O 2822 8.00 N 2704 7.00 C 9426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 467.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 8 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 50.4% alpha, 10.2% beta 8 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.608A pdb=" N LEU D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.732A pdb=" N LEU E 18 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 36 through 41 removed outlier: 3.732A pdb=" N LYS E 40 " --> pdb=" O HIS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 129 through 139 removed outlier: 3.585A pdb=" N LEU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 175 removed outlier: 3.746A pdb=" N ASP E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'F' and resid 37 through 49 removed outlier: 3.953A pdb=" N CYS F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 81 removed outlier: 3.926A pdb=" N THR F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 103 removed outlier: 3.635A pdb=" N VAL F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 147 Processing helix chain 'F' and resid 154 through 158 removed outlier: 4.002A pdb=" N LYS F 157 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 removed outlier: 3.954A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.796A pdb=" N ILE F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.577A pdb=" N LEU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 251 removed outlier: 3.664A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 259 through 262 removed outlier: 3.589A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 259 through 262' Processing helix chain 'F' and resid 263 through 275 removed outlier: 3.554A pdb=" N LEU F 267 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 292 removed outlier: 4.226A pdb=" N VAL F 285 " --> pdb=" O LEU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 316 removed outlier: 3.964A pdb=" N PHE F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.720A pdb=" N LYS F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.608A pdb=" N LEU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.731A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.733A pdb=" N LYS B 40 " --> pdb=" O HIS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.585A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.747A pdb=" N ASP B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.953A pdb=" N CYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 81 removed outlier: 3.926A pdb=" N THR C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 91 through 103 removed outlier: 3.636A pdb=" N VAL C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.001A pdb=" N LYS C 157 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.954A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.796A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.576A pdb=" N LEU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 removed outlier: 3.665A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 259 through 262 removed outlier: 3.587A pdb=" N VAL C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 263 through 275 removed outlier: 3.554A pdb=" N LEU C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 removed outlier: 4.226A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 316 removed outlier: 3.964A pdb=" N PHE C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 removed outlier: 3.720A pdb=" N LYS C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 62 through 70 Processing sheet with id=AA2, first strand: chain 'D' and resid 118 through 121 Processing sheet with id=AA3, first strand: chain 'D' and resid 246 through 247 Processing sheet with id=AA4, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AA5, first strand: chain 'E' and resid 89 through 94 removed outlier: 3.651A pdb=" N GLY E 64 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 121 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 243 through 247 removed outlier: 5.294A pdb=" N GLY E 244 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE E 232 " --> pdb=" O GLY E 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 250 through 251 removed outlier: 4.075A pdb=" N GLN E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AB2, first strand: chain 'A' and resid 255 through 258 Processing sheet with id=AB3, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.650A pdb=" N GLY B 64 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 121 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 247 removed outlier: 5.293A pdb=" N GLY B 244 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE B 232 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 250 through 251 removed outlier: 4.075A pdb=" N GLN B 250 " --> pdb=" O LEU B 257 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2176 1.31 - 1.43: 4825 1.43 - 1.56: 8451 1.56 - 1.68: 162 1.68 - 1.81: 62 Bond restraints: 15676 Sorted by residual: bond pdb=" CAN KLQ B 304 " pdb=" CBC KLQ B 304 " ideal model delta sigma weight residual 1.524 1.266 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" CAN KLQ E 304 " pdb=" CBC KLQ E 304 " ideal model delta sigma weight residual 1.524 1.267 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" CAN KLQ B 304 " pdb=" CBB KLQ B 304 " ideal model delta sigma weight residual 1.520 1.284 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAN KLQ E 304 " pdb=" CBB KLQ E 304 " ideal model delta sigma weight residual 1.520 1.284 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" CBD KLQ B 304 " pdb=" NBE KLQ B 304 " ideal model delta sigma weight residual 1.457 1.670 -0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 15671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 21634 3.98 - 7.97: 44 7.97 - 11.95: 6 11.95 - 15.94: 2 15.94 - 19.92: 2 Bond angle restraints: 21688 Sorted by residual: angle pdb=" CBB KLQ B 304 " pdb=" CAN KLQ B 304 " pdb=" CBC KLQ B 304 " ideal model delta sigma weight residual 99.19 119.11 -19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" CBB KLQ E 304 " pdb=" CAN KLQ E 304 " pdb=" CBC KLQ E 304 " ideal model delta sigma weight residual 99.19 119.11 -19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" CA PRO C 93 " pdb=" N PRO C 93 " pdb=" CD PRO C 93 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.86e+01 angle pdb=" CA PRO F 93 " pdb=" N PRO F 93 " pdb=" CD PRO F 93 " ideal model delta sigma weight residual 112.00 104.56 7.44 1.40e+00 5.10e-01 2.82e+01 angle pdb=" CBD KLQ E 304 " pdb=" CAO KLQ E 304 " pdb=" NBF KLQ E 304 " ideal model delta sigma weight residual 109.90 123.75 -13.85 3.00e+00 1.11e-01 2.13e+01 ... (remaining 21683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 7831 16.87 - 33.74: 877 33.74 - 50.60: 374 50.60 - 67.47: 96 67.47 - 84.34: 18 Dihedral angle restraints: 9196 sinusoidal: 4280 harmonic: 4916 Sorted by residual: dihedral pdb=" CA PRO F 93 " pdb=" C PRO F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO C 93 " pdb=" C PRO C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 230 " pdb=" C TYR A 230 " pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2093 0.053 - 0.106: 271 0.106 - 0.159: 40 0.159 - 0.212: 2 0.212 - 0.265: 6 Chirality restraints: 2412 Sorted by residual: chirality pdb=" CBB KLQ B 304 " pdb=" CAL KLQ B 304 " pdb=" CAN KLQ B 304 " pdb=" OAQ KLQ B 304 " both_signs ideal model delta sigma weight residual False 2.70 2.44 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CBB KLQ E 304 " pdb=" CAL KLQ E 304 " pdb=" CAN KLQ E 304 " pdb=" OAQ KLQ E 304 " both_signs ideal model delta sigma weight residual False 2.70 2.44 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CBD KLQ B 304 " pdb=" CAO KLQ B 304 " pdb=" NBE KLQ B 304 " pdb=" OAQ KLQ B 304 " both_signs ideal model delta sigma weight residual False 2.41 2.67 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2409 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 92 " -0.099 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO C 93 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 92 " 0.098 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO F 93 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 125 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.038 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 32 2.31 - 2.96: 6401 2.96 - 3.61: 21755 3.61 - 4.25: 34385 4.25 - 4.90: 56223 Nonbonded interactions: 118796 Sorted by model distance: nonbonded pdb="MG MG E 302 " pdb=" OAB KLQ E 304 " model vdw 1.666 2.170 nonbonded pdb="MG MG B 302 " pdb=" OAB KLQ B 304 " model vdw 1.667 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.785 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.874 2.170 ... (remaining 118791 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' } ncs_group { reference = chain 'E' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'C' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.258 15692 Z= 0.326 Angle : 0.788 42.568 21696 Z= 0.322 Chirality : 0.039 0.265 2412 Planarity : 0.006 0.147 2466 Dihedral : 17.346 84.340 5984 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.40 (0.21), residues: 1640 helix: 1.33 (0.20), residues: 748 sheet: -0.18 (0.33), residues: 220 loop : -0.74 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 142 TYR 0.011 0.001 TYR C 158 PHE 0.014 0.001 PHE C 274 TRP 0.008 0.001 TRP C 65 HIS 0.009 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00665 (15676) covalent geometry : angle 0.62966 (21688) hydrogen bonds : bond 0.17985 ( 655) hydrogen bonds : angle 6.48232 ( 1881) metal coordination : bond 0.01010 ( 16) metal coordination : angle 24.69507 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LEU cc_start: 0.7796 (tp) cc_final: 0.7483 (tt) REVERT: D 36 HIS cc_start: 0.6613 (t70) cc_final: 0.6275 (t70) REVERT: D 165 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6824 (mmmt) REVERT: D 167 LEU cc_start: 0.8451 (mt) cc_final: 0.8061 (mt) REVERT: E 26 THR cc_start: 0.8081 (p) cc_final: 0.7740 (p) REVERT: E 39 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7722 (mmm160) REVERT: E 53 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7968 (ttm-80) REVERT: E 90 SER cc_start: 0.8020 (t) cc_final: 0.7714 (p) REVERT: E 164 LEU cc_start: 0.8516 (tp) cc_final: 0.8280 (tp) REVERT: E 172 PHE cc_start: 0.8457 (m-10) cc_final: 0.8199 (m-80) REVERT: F 32 ASP cc_start: 0.6853 (m-30) cc_final: 0.6589 (m-30) REVERT: F 48 GLN cc_start: 0.7602 (tt0) cc_final: 0.7357 (tt0) REVERT: F 67 GLU cc_start: 0.6723 (tp30) cc_final: 0.5222 (tp30) REVERT: F 69 LYS cc_start: 0.7800 (tttt) cc_final: 0.7581 (tttp) REVERT: F 159 ILE cc_start: 0.6539 (mm) cc_final: 0.5906 (tt) REVERT: F 168 LEU cc_start: 0.8188 (tp) cc_final: 0.7880 (tp) REVERT: F 228 LEU cc_start: 0.8312 (mt) cc_final: 0.8029 (mt) REVERT: F 241 GLU cc_start: 0.5500 (tm-30) cc_final: 0.5054 (tm-30) REVERT: F 245 ILE cc_start: 0.7406 (mt) cc_final: 0.7119 (mt) REVERT: F 256 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7452 (ptpt) REVERT: A 119 ILE cc_start: 0.7445 (tt) cc_final: 0.7219 (tt) REVERT: A 165 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6276 (mmmt) REVERT: A 168 LEU cc_start: 0.7336 (mt) cc_final: 0.6948 (mt) REVERT: A 200 CYS cc_start: 0.6948 (p) cc_final: 0.6706 (p) REVERT: B 99 SER cc_start: 0.7288 (m) cc_final: 0.6957 (p) REVERT: B 130 GLN cc_start: 0.6414 (tp-100) cc_final: 0.6182 (tp-100) REVERT: B 150 ASN cc_start: 0.8088 (t0) cc_final: 0.7855 (t0) REVERT: C 134 LEU cc_start: 0.7094 (mp) cc_final: 0.6881 (mm) REVERT: C 149 ASP cc_start: 0.7215 (m-30) cc_final: 0.6967 (m-30) REVERT: C 196 LEU cc_start: 0.7562 (mp) cc_final: 0.7321 (mt) REVERT: C 204 ILE cc_start: 0.8413 (tp) cc_final: 0.7682 (tp) REVERT: C 208 PHE cc_start: 0.6614 (m-10) cc_final: 0.6338 (m-80) REVERT: C 256 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7642 (ptpt) REVERT: C 263 TYR cc_start: 0.5717 (p90) cc_final: 0.5332 (p90) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.1530 time to fit residues: 118.0223 Evaluate side-chains 516 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 ASN E 195 ASN E 201 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS A 161 ASN B 41 ASN B 192 ASN B 195 ASN C 44 GLN C 133 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112542 restraints weight = 25935.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116280 restraints weight = 12126.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118613 restraints weight = 7382.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120097 restraints weight = 5387.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120988 restraints weight = 4423.428| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15692 Z= 0.209 Angle : 0.633 8.542 21696 Z= 0.331 Chirality : 0.043 0.202 2412 Planarity : 0.005 0.062 2466 Dihedral : 18.842 78.533 2758 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 11.68 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.32 (0.21), residues: 1640 helix: 1.06 (0.19), residues: 768 sheet: 0.05 (0.32), residues: 220 loop : -0.68 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 70 TYR 0.024 0.002 TYR F 263 PHE 0.028 0.002 PHE F 246 TRP 0.010 0.001 TRP B 205 HIS 0.021 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00452 (15676) covalent geometry : angle 0.62857 (21688) hydrogen bonds : bond 0.05258 ( 655) hydrogen bonds : angle 4.92620 ( 1881) metal coordination : bond 0.03391 ( 16) metal coordination : angle 3.98358 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 527 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8031 (mmmt) REVERT: D 167 LEU cc_start: 0.8448 (mt) cc_final: 0.8125 (mt) REVERT: D 170 LYS cc_start: 0.8524 (mttt) cc_final: 0.8144 (mttt) REVERT: D 190 THR cc_start: 0.8440 (p) cc_final: 0.8214 (p) REVERT: D 192 ASN cc_start: 0.8854 (m-40) cc_final: 0.8605 (m-40) REVERT: D 216 ILE cc_start: 0.7971 (mt) cc_final: 0.7244 (mp) REVERT: D 232 PHE cc_start: 0.8142 (p90) cc_final: 0.7883 (p90) REVERT: D 273 LEU cc_start: 0.8459 (mt) cc_final: 0.8165 (mm) REVERT: E 27 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 33 HIS cc_start: 0.7511 (m-70) cc_final: 0.7126 (m-70) REVERT: E 36 HIS cc_start: 0.7672 (t70) cc_final: 0.7435 (t70) REVERT: E 53 ARG cc_start: 0.8595 (tpp80) cc_final: 0.7961 (ttm170) REVERT: E 90 SER cc_start: 0.8205 (t) cc_final: 0.7697 (p) REVERT: E 101 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7002 (mp0) REVERT: E 172 PHE cc_start: 0.8880 (m-10) cc_final: 0.8632 (m-80) REVERT: E 180 MET cc_start: 0.7195 (tpp) cc_final: 0.6975 (tpp) REVERT: E 202 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7767 (mttm) REVERT: E 232 PHE cc_start: 0.8188 (p90) cc_final: 0.7791 (p90) REVERT: F 47 ARG cc_start: 0.7309 (mtp180) cc_final: 0.7001 (mtp-110) REVERT: F 67 GLU cc_start: 0.7676 (tp30) cc_final: 0.7454 (tp30) REVERT: F 101 VAL cc_start: 0.8525 (t) cc_final: 0.8170 (m) REVERT: F 159 ILE cc_start: 0.7132 (mm) cc_final: 0.6858 (mt) REVERT: F 168 LEU cc_start: 0.8775 (tp) cc_final: 0.8427 (tp) REVERT: F 202 LYS cc_start: 0.7408 (mttt) cc_final: 0.7082 (mttt) REVERT: F 211 PHE cc_start: 0.8387 (t80) cc_final: 0.8182 (t80) REVERT: F 225 LEU cc_start: 0.8394 (mt) cc_final: 0.8118 (mt) REVERT: F 226 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7087 (mm-30) REVERT: F 228 LEU cc_start: 0.8834 (mt) cc_final: 0.8461 (mt) REVERT: F 241 GLU cc_start: 0.6302 (tm-30) cc_final: 0.5630 (tm-30) REVERT: F 245 ILE cc_start: 0.8241 (mt) cc_final: 0.7751 (mt) REVERT: F 256 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7317 (ptpt) REVERT: F 259 SER cc_start: 0.8183 (m) cc_final: 0.7888 (t) REVERT: F 283 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7690 (tm-30) REVERT: F 287 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6360 (ptp) REVERT: A 7 LEU cc_start: 0.8323 (tp) cc_final: 0.8119 (tt) REVERT: A 165 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7674 (mmmt) REVERT: A 170 LYS cc_start: 0.8388 (mttt) cc_final: 0.8084 (mttt) REVERT: A 197 LEU cc_start: 0.8011 (mt) cc_final: 0.7739 (mp) REVERT: A 204 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8193 (mtt90) REVERT: A 212 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7133 (mmm160) REVERT: B 9 SER cc_start: 0.8881 (t) cc_final: 0.8681 (t) REVERT: B 31 ILE cc_start: 0.8779 (mt) cc_final: 0.8364 (tt) REVERT: B 34 SER cc_start: 0.8373 (m) cc_final: 0.8128 (p) REVERT: B 70 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7918 (ttmm) REVERT: B 93 HIS cc_start: 0.8306 (p-80) cc_final: 0.8100 (p90) REVERT: B 133 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: B 170 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8542 (ttmt) REVERT: B 171 TYR cc_start: 0.8785 (m-10) cc_final: 0.8582 (m-10) REVERT: B 202 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7742 (mttm) REVERT: B 266 GLN cc_start: 0.8259 (tt0) cc_final: 0.8003 (tt0) REVERT: C 44 GLN cc_start: 0.7835 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 48 GLN cc_start: 0.8148 (tt0) cc_final: 0.7621 (tt0) REVERT: C 69 LYS cc_start: 0.8064 (tptm) cc_final: 0.7302 (tptt) REVERT: C 101 VAL cc_start: 0.8263 (t) cc_final: 0.8059 (m) REVERT: C 171 PHE cc_start: 0.7960 (m-80) cc_final: 0.7631 (t80) REVERT: C 177 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7218 (mpp80) REVERT: C 181 PHE cc_start: 0.8731 (m-10) cc_final: 0.8519 (m-10) REVERT: C 202 LYS cc_start: 0.7855 (mttt) cc_final: 0.7641 (mttt) REVERT: C 204 ILE cc_start: 0.8468 (tp) cc_final: 0.8163 (tp) REVERT: C 206 ASN cc_start: 0.7001 (t0) cc_final: 0.6688 (t0) REVERT: C 241 GLU cc_start: 0.5968 (tm-30) cc_final: 0.5714 (tm-30) REVERT: C 263 TYR cc_start: 0.6569 (p90) cc_final: 0.6135 (p90) outliers start: 27 outliers final: 22 residues processed: 534 average time/residue: 0.1559 time to fit residues: 114.5803 Evaluate side-chains 534 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 510 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 120 optimal weight: 0.0980 chunk 125 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 139 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 HIS E 30 ASN E 175 ASN E 266 GLN F 44 GLN F 102 ASN B 123 ASN B 130 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112585 restraints weight = 25966.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116431 restraints weight = 11954.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118823 restraints weight = 7229.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120331 restraints weight = 5268.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121239 restraints weight = 4330.953| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15692 Z= 0.139 Angle : 0.574 9.477 21696 Z= 0.294 Chirality : 0.041 0.225 2412 Planarity : 0.004 0.050 2466 Dihedral : 18.711 78.055 2758 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.34 % Allowed : 15.80 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.36 (0.21), residues: 1640 helix: 1.09 (0.19), residues: 764 sheet: 0.19 (0.33), residues: 220 loop : -0.67 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 70 TYR 0.021 0.002 TYR C 158 PHE 0.024 0.002 PHE C 150 TRP 0.013 0.001 TRP B 205 HIS 0.014 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00301 (15676) covalent geometry : angle 0.57101 (21688) hydrogen bonds : bond 0.04311 ( 655) hydrogen bonds : angle 4.64578 ( 1881) metal coordination : bond 0.01350 ( 16) metal coordination : angle 2.88135 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 522 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 165 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8025 (mmmt) REVERT: D 170 LYS cc_start: 0.8540 (mttt) cc_final: 0.8110 (mttt) REVERT: D 192 ASN cc_start: 0.8832 (m-40) cc_final: 0.8611 (m-40) REVERT: D 212 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6999 (mmm160) REVERT: D 216 ILE cc_start: 0.7711 (mt) cc_final: 0.7408 (mm) REVERT: D 273 LEU cc_start: 0.8463 (mt) cc_final: 0.8180 (mm) REVERT: E 27 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7510 (mt-10) REVERT: E 30 ASN cc_start: 0.7948 (m-40) cc_final: 0.7651 (m-40) REVERT: E 31 ILE cc_start: 0.8684 (mt) cc_final: 0.8145 (tp) REVERT: E 34 SER cc_start: 0.8295 (m) cc_final: 0.7991 (p) REVERT: E 36 HIS cc_start: 0.7736 (t70) cc_final: 0.7444 (t70) REVERT: E 53 ARG cc_start: 0.8564 (tpp80) cc_final: 0.7947 (ttm170) REVERT: E 66 ILE cc_start: 0.8547 (mt) cc_final: 0.8216 (tp) REVERT: E 90 SER cc_start: 0.8179 (t) cc_final: 0.7659 (p) REVERT: E 101 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6961 (mp0) REVERT: E 180 MET cc_start: 0.7213 (tpp) cc_final: 0.6995 (tpp) REVERT: E 202 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7763 (mttm) REVERT: E 232 PHE cc_start: 0.8166 (p90) cc_final: 0.7768 (p90) REVERT: F 47 ARG cc_start: 0.7262 (mtp180) cc_final: 0.7014 (mtp-110) REVERT: F 67 GLU cc_start: 0.7611 (tp30) cc_final: 0.6568 (tp30) REVERT: F 70 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7103 (ttp80) REVERT: F 101 VAL cc_start: 0.8572 (t) cc_final: 0.8221 (m) REVERT: F 134 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7381 (mm) REVERT: F 159 ILE cc_start: 0.7193 (mm) cc_final: 0.6789 (mt) REVERT: F 168 LEU cc_start: 0.8785 (tp) cc_final: 0.8457 (tp) REVERT: F 171 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (t80) REVERT: F 192 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7427 (mmmt) REVERT: F 202 LYS cc_start: 0.7429 (mttt) cc_final: 0.7099 (mttt) REVERT: F 203 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8179 (tm-30) REVERT: F 226 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6874 (mm-30) REVERT: F 228 LEU cc_start: 0.8844 (mt) cc_final: 0.8453 (mt) REVERT: F 241 GLU cc_start: 0.6321 (tm-30) cc_final: 0.5588 (tm-30) REVERT: F 245 ILE cc_start: 0.8207 (mt) cc_final: 0.7659 (mt) REVERT: F 256 LYS cc_start: 0.7813 (ptpt) cc_final: 0.7309 (ptpt) REVERT: F 259 SER cc_start: 0.8239 (m) cc_final: 0.7946 (t) REVERT: F 287 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6385 (ptp) REVERT: A 7 LEU cc_start: 0.8388 (tp) cc_final: 0.8109 (tt) REVERT: A 9 SER cc_start: 0.8673 (m) cc_final: 0.8314 (p) REVERT: A 165 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7703 (mmmt) REVERT: A 170 LYS cc_start: 0.8496 (mttt) cc_final: 0.8109 (mttt) REVERT: A 212 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7164 (mmm160) REVERT: B 9 SER cc_start: 0.8880 (t) cc_final: 0.8670 (t) REVERT: B 27 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 31 ILE cc_start: 0.8731 (mt) cc_final: 0.8392 (mp) REVERT: B 34 SER cc_start: 0.8375 (m) cc_final: 0.8135 (p) REVERT: B 202 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7754 (mttm) REVERT: B 268 ILE cc_start: 0.8486 (mm) cc_final: 0.8038 (tp) REVERT: C 44 GLN cc_start: 0.7941 (tt0) cc_final: 0.7633 (tm-30) REVERT: C 48 GLN cc_start: 0.8175 (tt0) cc_final: 0.7638 (tm-30) REVERT: C 69 LYS cc_start: 0.8022 (tptm) cc_final: 0.7244 (tptt) REVERT: C 134 LEU cc_start: 0.7848 (mm) cc_final: 0.7459 (mm) REVERT: C 165 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7287 (mm) REVERT: C 171 PHE cc_start: 0.7965 (m-80) cc_final: 0.7623 (t80) REVERT: C 177 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6942 (mtm180) REVERT: C 202 LYS cc_start: 0.7835 (mttt) cc_final: 0.7626 (mttt) REVERT: C 203 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8099 (tm-30) REVERT: C 204 ILE cc_start: 0.8422 (tp) cc_final: 0.8173 (tp) REVERT: C 206 ASN cc_start: 0.7064 (t0) cc_final: 0.6735 (t0) REVERT: C 241 GLU cc_start: 0.6170 (tm-30) cc_final: 0.5678 (tm-30) REVERT: C 263 TYR cc_start: 0.6542 (p90) cc_final: 0.6161 (p90) REVERT: C 305 LEU cc_start: 0.8015 (mm) cc_final: 0.7776 (mm) outliers start: 34 outliers final: 19 residues processed: 534 average time/residue: 0.1518 time to fit residues: 111.7754 Evaluate side-chains 529 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 506 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 154 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 HIS E 133 GLN F 306 ASN B 123 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110911 restraints weight = 26003.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114688 restraints weight = 12025.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117066 restraints weight = 7298.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118555 restraints weight = 5304.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119360 restraints weight = 4359.804| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15692 Z= 0.181 Angle : 0.592 11.024 21696 Z= 0.306 Chirality : 0.043 0.236 2412 Planarity : 0.004 0.037 2466 Dihedral : 18.845 79.407 2758 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 17.51 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.34 (0.21), residues: 1640 helix: 1.07 (0.19), residues: 770 sheet: 0.19 (0.33), residues: 220 loop : -0.71 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 210 TYR 0.026 0.002 TYR C 158 PHE 0.027 0.002 PHE C 150 TRP 0.014 0.001 TRP C 65 HIS 0.009 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00392 (15676) covalent geometry : angle 0.58672 (21688) hydrogen bonds : bond 0.04268 ( 655) hydrogen bonds : angle 4.60153 ( 1881) metal coordination : bond 0.02612 ( 16) metal coordination : angle 4.01602 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 531 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7394 (ptpp) cc_final: 0.6966 (ptpp) REVERT: D 165 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8034 (mmmt) REVERT: D 212 ARG cc_start: 0.7386 (mmm160) cc_final: 0.7049 (mmm160) REVERT: D 216 ILE cc_start: 0.7844 (mt) cc_final: 0.7520 (mm) REVERT: D 273 LEU cc_start: 0.8528 (mt) cc_final: 0.8314 (mm) REVERT: D 275 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7362 (ttt-90) REVERT: E 27 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7415 (mt-10) REVERT: E 30 ASN cc_start: 0.8006 (m-40) cc_final: 0.7633 (m-40) REVERT: E 31 ILE cc_start: 0.8668 (mt) cc_final: 0.8297 (mp) REVERT: E 34 SER cc_start: 0.8308 (m) cc_final: 0.8051 (p) REVERT: E 36 HIS cc_start: 0.7716 (t70) cc_final: 0.7416 (t70) REVERT: E 53 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8162 (ttm-80) REVERT: E 90 SER cc_start: 0.8196 (t) cc_final: 0.7686 (p) REVERT: E 101 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7037 (mp0) REVERT: E 178 LEU cc_start: 0.8663 (tp) cc_final: 0.8353 (tt) REVERT: E 202 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7790 (mmtm) REVERT: F 44 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 47 ARG cc_start: 0.7226 (mtp180) cc_final: 0.7009 (mtp-110) REVERT: F 67 GLU cc_start: 0.7690 (tp30) cc_final: 0.6720 (tp30) REVERT: F 69 LYS cc_start: 0.8278 (tttt) cc_final: 0.7860 (tttp) REVERT: F 70 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7039 (ttp80) REVERT: F 76 MET cc_start: 0.6780 (mmm) cc_final: 0.6480 (mmm) REVERT: F 101 VAL cc_start: 0.8568 (t) cc_final: 0.8250 (m) REVERT: F 134 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7388 (mm) REVERT: F 168 LEU cc_start: 0.8852 (tp) cc_final: 0.8533 (tp) REVERT: F 171 PHE cc_start: 0.8258 (t80) cc_final: 0.7902 (t80) REVERT: F 192 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7470 (mmmt) REVERT: F 202 LYS cc_start: 0.7559 (mttt) cc_final: 0.7204 (mttt) REVERT: F 203 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8208 (tm-30) REVERT: F 226 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6835 (mm-30) REVERT: F 228 LEU cc_start: 0.8883 (mt) cc_final: 0.8456 (mt) REVERT: F 241 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5767 (tm-30) REVERT: F 245 ILE cc_start: 0.7995 (mt) cc_final: 0.7436 (mt) REVERT: F 256 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7415 (ptpt) REVERT: F 259 SER cc_start: 0.8247 (m) cc_final: 0.7867 (t) REVERT: A 7 LEU cc_start: 0.8363 (tp) cc_final: 0.8059 (tt) REVERT: A 9 SER cc_start: 0.8737 (m) cc_final: 0.8377 (p) REVERT: A 105 SER cc_start: 0.8055 (p) cc_final: 0.7833 (p) REVERT: A 119 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7172 (tt) REVERT: A 165 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7788 (mmmt) REVERT: A 168 LEU cc_start: 0.8349 (mt) cc_final: 0.7929 (mt) REVERT: A 172 PHE cc_start: 0.8123 (m-80) cc_final: 0.7916 (m-80) REVERT: A 212 ARG cc_start: 0.7567 (mmm160) cc_final: 0.7122 (mmm160) REVERT: B 27 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 31 ILE cc_start: 0.8739 (mt) cc_final: 0.8358 (mp) REVERT: B 34 SER cc_start: 0.8401 (m) cc_final: 0.8170 (p) REVERT: B 101 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6610 (mp0) REVERT: B 150 ASN cc_start: 0.8412 (t0) cc_final: 0.8173 (t0) REVERT: B 202 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7783 (mmtm) REVERT: B 243 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8270 (mmtp) REVERT: B 266 GLN cc_start: 0.8315 (tt0) cc_final: 0.8048 (tt0) REVERT: B 268 ILE cc_start: 0.8508 (mm) cc_final: 0.8057 (tp) REVERT: C 44 GLN cc_start: 0.8018 (tt0) cc_final: 0.7619 (tm-30) REVERT: C 48 GLN cc_start: 0.8173 (tt0) cc_final: 0.7655 (tm-30) REVERT: C 69 LYS cc_start: 0.8068 (tptm) cc_final: 0.7299 (tptt) REVERT: C 134 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7533 (mm) REVERT: C 171 PHE cc_start: 0.8048 (m-80) cc_final: 0.7711 (t80) REVERT: C 202 LYS cc_start: 0.7974 (mttt) cc_final: 0.7721 (mttt) REVERT: C 203 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8158 (tm-30) REVERT: C 206 ASN cc_start: 0.7275 (t0) cc_final: 0.6914 (t0) REVERT: C 241 GLU cc_start: 0.6214 (tm-30) cc_final: 0.5725 (tm-30) REVERT: C 263 TYR cc_start: 0.6704 (p90) cc_final: 0.6294 (p90) REVERT: C 305 LEU cc_start: 0.7953 (mm) cc_final: 0.7707 (mm) outliers start: 47 outliers final: 30 residues processed: 546 average time/residue: 0.1491 time to fit residues: 112.5363 Evaluate side-chains 550 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 517 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 GLN A 193 HIS A 246 GLN B 146 HIS ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111693 restraints weight = 25781.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115464 restraints weight = 11857.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117821 restraints weight = 7137.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119288 restraints weight = 5173.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120167 restraints weight = 4244.472| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15692 Z= 0.145 Angle : 0.569 10.476 21696 Z= 0.293 Chirality : 0.041 0.230 2412 Planarity : 0.004 0.033 2466 Dihedral : 18.805 82.764 2758 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.37 % Allowed : 19.30 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.43 (0.21), residues: 1640 helix: 1.18 (0.19), residues: 766 sheet: 0.19 (0.32), residues: 220 loop : -0.69 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 143 TYR 0.017 0.001 TYR C 199 PHE 0.025 0.002 PHE C 141 TRP 0.011 0.001 TRP F 131 HIS 0.007 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00320 (15676) covalent geometry : angle 0.56750 (21688) hydrogen bonds : bond 0.03846 ( 655) hydrogen bonds : angle 4.48292 ( 1881) metal coordination : bond 0.01737 ( 16) metal coordination : angle 2.12533 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 543 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 GLN cc_start: 0.7377 (tp40) cc_final: 0.7076 (mp10) REVERT: D 165 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8004 (mmmt) REVERT: D 170 LYS cc_start: 0.8535 (mttt) cc_final: 0.7823 (mttt) REVERT: D 186 VAL cc_start: 0.8547 (t) cc_final: 0.8224 (p) REVERT: D 212 ARG cc_start: 0.7350 (mmm160) cc_final: 0.7020 (mmm160) REVERT: D 246 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: D 273 LEU cc_start: 0.8538 (mt) cc_final: 0.8336 (mm) REVERT: D 275 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7368 (ttt-90) REVERT: E 30 ASN cc_start: 0.8016 (m-40) cc_final: 0.7639 (m-40) REVERT: E 31 ILE cc_start: 0.8679 (mt) cc_final: 0.8316 (mp) REVERT: E 34 SER cc_start: 0.8281 (m) cc_final: 0.8027 (p) REVERT: E 36 HIS cc_start: 0.7700 (t70) cc_final: 0.7373 (t70) REVERT: E 44 GLN cc_start: 0.8079 (mp10) cc_final: 0.7870 (mp10) REVERT: E 53 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8142 (ttm-80) REVERT: E 90 SER cc_start: 0.8174 (t) cc_final: 0.7654 (p) REVERT: E 101 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7017 (mp0) REVERT: E 178 LEU cc_start: 0.8654 (tp) cc_final: 0.8376 (tt) REVERT: E 202 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7737 (mmtm) REVERT: E 268 ILE cc_start: 0.8571 (mm) cc_final: 0.8166 (tp) REVERT: F 47 ARG cc_start: 0.7247 (mtp180) cc_final: 0.7045 (mtp-110) REVERT: F 67 GLU cc_start: 0.7692 (tp30) cc_final: 0.6579 (tp30) REVERT: F 69 LYS cc_start: 0.8278 (tttt) cc_final: 0.7813 (tttp) REVERT: F 70 ARG cc_start: 0.7591 (ttp80) cc_final: 0.6998 (ttp80) REVERT: F 76 MET cc_start: 0.6710 (mmm) cc_final: 0.6458 (mmm) REVERT: F 101 VAL cc_start: 0.8580 (t) cc_final: 0.8282 (m) REVERT: F 134 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7400 (mm) REVERT: F 168 LEU cc_start: 0.8856 (tp) cc_final: 0.8537 (tp) REVERT: F 171 PHE cc_start: 0.8238 (t80) cc_final: 0.7996 (t80) REVERT: F 192 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7516 (mmmt) REVERT: F 202 LYS cc_start: 0.7629 (mttt) cc_final: 0.7260 (mttt) REVERT: F 225 LEU cc_start: 0.8353 (mt) cc_final: 0.7781 (mt) REVERT: F 226 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6822 (mm-30) REVERT: F 228 LEU cc_start: 0.8879 (mt) cc_final: 0.8488 (mt) REVERT: F 241 GLU cc_start: 0.6463 (tm-30) cc_final: 0.5671 (tm-30) REVERT: F 245 ILE cc_start: 0.8000 (mt) cc_final: 0.7410 (mt) REVERT: F 256 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7369 (ptpt) REVERT: F 259 SER cc_start: 0.8257 (m) cc_final: 0.7859 (t) REVERT: A 7 LEU cc_start: 0.8381 (tp) cc_final: 0.8121 (tt) REVERT: A 9 SER cc_start: 0.8716 (m) cc_final: 0.8278 (p) REVERT: A 19 THR cc_start: 0.8262 (m) cc_final: 0.7847 (p) REVERT: A 97 GLU cc_start: 0.7503 (tt0) cc_final: 0.7283 (tt0) REVERT: A 119 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7118 (tt) REVERT: A 133 GLN cc_start: 0.7276 (tp40) cc_final: 0.7003 (mp10) REVERT: A 142 ARG cc_start: 0.6866 (ptt-90) cc_final: 0.6627 (ptt-90) REVERT: A 165 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7788 (mmmt) REVERT: A 168 LEU cc_start: 0.8328 (mt) cc_final: 0.7904 (mt) REVERT: A 172 PHE cc_start: 0.8146 (m-80) cc_final: 0.7925 (m-80) REVERT: A 212 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7151 (mmm160) REVERT: A 246 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: B 27 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 31 ILE cc_start: 0.8778 (mt) cc_final: 0.8409 (mp) REVERT: B 34 SER cc_start: 0.8426 (m) cc_final: 0.8184 (p) REVERT: B 133 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: B 202 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7740 (mmtm) REVERT: B 243 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8151 (mmtm) REVERT: C 44 GLN cc_start: 0.8032 (tt0) cc_final: 0.7634 (tm-30) REVERT: C 48 GLN cc_start: 0.8161 (tt0) cc_final: 0.7717 (tm-30) REVERT: C 69 LYS cc_start: 0.8099 (tptm) cc_final: 0.7197 (tptt) REVERT: C 128 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 134 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7405 (mm) REVERT: C 165 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7272 (mm) REVERT: C 171 PHE cc_start: 0.7991 (m-80) cc_final: 0.7667 (t80) REVERT: C 175 ASP cc_start: 0.7712 (p0) cc_final: 0.7092 (p0) REVERT: C 179 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7357 (mtm110) REVERT: C 201 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.7063 (mtm-85) REVERT: C 202 LYS cc_start: 0.8045 (mttt) cc_final: 0.7779 (mttt) REVERT: C 210 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7106 (mtm180) REVERT: C 226 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7257 (mt-10) REVERT: C 241 GLU cc_start: 0.6323 (tm-30) cc_final: 0.5715 (tm-30) REVERT: C 263 TYR cc_start: 0.6663 (p90) cc_final: 0.6264 (p90) outliers start: 49 outliers final: 27 residues processed: 557 average time/residue: 0.1505 time to fit residues: 115.7724 Evaluate side-chains 561 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 527 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 127 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 HIS D 250 GLN E 118 HIS E 133 GLN E 146 HIS F 206 ASN A 30 ASN B 68 HIS ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109097 restraints weight = 25697.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112832 restraints weight = 11912.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115156 restraints weight = 7231.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116604 restraints weight = 5277.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117450 restraints weight = 4355.216| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15692 Z= 0.229 Angle : 0.625 10.554 21696 Z= 0.323 Chirality : 0.044 0.238 2412 Planarity : 0.004 0.034 2466 Dihedral : 19.038 84.330 2758 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 20.19 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.25 (0.21), residues: 1640 helix: 1.04 (0.19), residues: 772 sheet: 0.07 (0.33), residues: 220 loop : -0.80 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 143 TYR 0.015 0.002 TYR E 169 PHE 0.026 0.002 PHE C 141 TRP 0.013 0.002 TRP B 205 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00485 (15676) covalent geometry : angle 0.61747 (21688) hydrogen bonds : bond 0.04413 ( 655) hydrogen bonds : angle 4.63851 ( 1881) metal coordination : bond 0.03499 ( 16) metal coordination : angle 5.20127 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 538 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7416 (ptpp) cc_final: 0.6994 (ptpp) REVERT: D 133 GLN cc_start: 0.7394 (tp40) cc_final: 0.7099 (mp10) REVERT: D 142 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6575 (ptt-90) REVERT: D 165 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7998 (mmmt) REVERT: D 170 LYS cc_start: 0.8515 (mttt) cc_final: 0.7857 (mttt) REVERT: D 186 VAL cc_start: 0.8610 (t) cc_final: 0.8273 (p) REVERT: D 212 ARG cc_start: 0.7373 (mmm160) cc_final: 0.7089 (mmm160) REVERT: D 275 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7440 (ttt-90) REVERT: E 27 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7288 (mt-10) REVERT: E 31 ILE cc_start: 0.8691 (mt) cc_final: 0.8209 (tt) REVERT: E 34 SER cc_start: 0.8306 (m) cc_final: 0.8052 (p) REVERT: E 36 HIS cc_start: 0.7701 (t70) cc_final: 0.7405 (t70) REVERT: E 47 MET cc_start: 0.8054 (mmm) cc_final: 0.7707 (mmm) REVERT: E 49 ARG cc_start: 0.6929 (mtm180) cc_final: 0.6684 (mtm180) REVERT: E 53 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8180 (ttm-80) REVERT: E 70 LYS cc_start: 0.8292 (ttmm) cc_final: 0.8010 (ttmm) REVERT: E 90 SER cc_start: 0.8197 (t) cc_final: 0.7701 (p) REVERT: E 101 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7060 (mp0) REVERT: E 178 LEU cc_start: 0.8707 (tp) cc_final: 0.8392 (tt) REVERT: E 201 GLN cc_start: 0.8679 (mm110) cc_final: 0.8301 (mm-40) REVERT: E 202 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7698 (mmtm) REVERT: E 268 ILE cc_start: 0.8555 (mm) cc_final: 0.8137 (tp) REVERT: F 44 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7634 (tm-30) REVERT: F 48 GLN cc_start: 0.8199 (tt0) cc_final: 0.7741 (tt0) REVERT: F 67 GLU cc_start: 0.7764 (tp30) cc_final: 0.6585 (tp30) REVERT: F 69 LYS cc_start: 0.8409 (tttt) cc_final: 0.7732 (tttp) REVERT: F 70 ARG cc_start: 0.7631 (ttp80) cc_final: 0.6965 (ttp80) REVERT: F 76 MET cc_start: 0.6801 (mmm) cc_final: 0.6474 (mmm) REVERT: F 101 VAL cc_start: 0.8610 (t) cc_final: 0.8274 (m) REVERT: F 134 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7388 (mm) REVERT: F 159 ILE cc_start: 0.7365 (mm) cc_final: 0.7003 (mt) REVERT: F 192 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7558 (mmmt) REVERT: F 202 LYS cc_start: 0.7830 (mttt) cc_final: 0.7400 (mttt) REVERT: F 225 LEU cc_start: 0.8416 (mt) cc_final: 0.7934 (mt) REVERT: F 226 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6932 (mm-30) REVERT: F 228 LEU cc_start: 0.8921 (mt) cc_final: 0.8481 (mt) REVERT: F 241 GLU cc_start: 0.6507 (tm-30) cc_final: 0.5677 (tm-30) REVERT: F 245 ILE cc_start: 0.8059 (mt) cc_final: 0.7487 (mt) REVERT: F 259 SER cc_start: 0.8282 (m) cc_final: 0.7896 (t) REVERT: A 9 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8443 (t) REVERT: A 30 ASN cc_start: 0.7629 (t0) cc_final: 0.7406 (t0) REVERT: A 123 ASN cc_start: 0.8259 (t0) cc_final: 0.7867 (t0) REVERT: A 136 CYS cc_start: 0.7001 (p) cc_final: 0.6716 (p) REVERT: A 165 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7851 (mmmt) REVERT: A 168 LEU cc_start: 0.8374 (mt) cc_final: 0.7983 (mt) REVERT: A 212 ARG cc_start: 0.7526 (mmm160) cc_final: 0.7025 (mmm160) REVERT: B 31 ILE cc_start: 0.8739 (mt) cc_final: 0.8425 (mt) REVERT: B 34 SER cc_start: 0.8433 (m) cc_final: 0.8191 (p) REVERT: B 53 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8008 (ttm-80) REVERT: B 96 ARG cc_start: 0.7470 (pmt170) cc_final: 0.6668 (pmt170) REVERT: B 101 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6862 (mp0) REVERT: B 133 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: B 202 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7868 (mmtm) REVERT: B 243 LYS cc_start: 0.8443 (mmtp) cc_final: 0.8030 (mmtm) REVERT: B 268 ILE cc_start: 0.8540 (mm) cc_final: 0.8067 (tp) REVERT: C 44 GLN cc_start: 0.8096 (tt0) cc_final: 0.7702 (tm-30) REVERT: C 48 GLN cc_start: 0.8177 (tt0) cc_final: 0.7664 (tm-30) REVERT: C 69 LYS cc_start: 0.8014 (tptm) cc_final: 0.7588 (tppt) REVERT: C 128 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 134 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (mm) REVERT: C 165 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7229 (mm) REVERT: C 171 PHE cc_start: 0.7918 (m-80) cc_final: 0.7623 (t80) REVERT: C 175 ASP cc_start: 0.7803 (p0) cc_final: 0.7199 (p0) REVERT: C 177 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7292 (mtm180) REVERT: C 179 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7410 (mtm110) REVERT: C 202 LYS cc_start: 0.8088 (mttt) cc_final: 0.7828 (mttt) REVERT: C 210 ARG cc_start: 0.7402 (mtt90) cc_final: 0.7013 (mtm180) REVERT: C 241 GLU cc_start: 0.6301 (tm-30) cc_final: 0.5658 (tm-30) REVERT: C 263 TYR cc_start: 0.6950 (p90) cc_final: 0.6524 (p90) REVERT: C 301 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7232 (mm-30) outliers start: 56 outliers final: 35 residues processed: 558 average time/residue: 0.1601 time to fit residues: 122.6097 Evaluate side-chains 578 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 537 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 HIS D 209 HIS D 246 GLN D 250 GLN E 118 HIS E 133 GLN F 206 ASN F 217 HIS A 133 GLN A 228 HIS A 246 GLN B 68 HIS B 177 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 306 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111013 restraints weight = 25531.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114734 restraints weight = 11783.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117088 restraints weight = 7138.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118552 restraints weight = 5186.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119449 restraints weight = 4270.816| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15692 Z= 0.144 Angle : 0.602 9.875 21696 Z= 0.308 Chirality : 0.042 0.157 2412 Planarity : 0.004 0.036 2466 Dihedral : 18.954 84.052 2758 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.43 % Allowed : 22.46 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.37 (0.21), residues: 1640 helix: 1.12 (0.19), residues: 770 sheet: 0.19 (0.33), residues: 200 loop : -0.70 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 210 TYR 0.015 0.001 TYR F 269 PHE 0.027 0.002 PHE C 141 TRP 0.011 0.001 TRP E 205 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00320 (15676) covalent geometry : angle 0.60074 (21688) hydrogen bonds : bond 0.03870 ( 655) hydrogen bonds : angle 4.56426 ( 1881) metal coordination : bond 0.01721 ( 16) metal coordination : angle 1.94005 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 533 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7359 (ptpp) cc_final: 0.6924 (ptpp) REVERT: D 133 GLN cc_start: 0.7383 (tp40) cc_final: 0.7088 (mp10) REVERT: D 142 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6470 (ptt-90) REVERT: D 165 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7966 (mmmt) REVERT: D 170 LYS cc_start: 0.8510 (mttt) cc_final: 0.7808 (mttt) REVERT: D 186 VAL cc_start: 0.8570 (t) cc_final: 0.8255 (p) REVERT: D 204 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8363 (mtt90) REVERT: D 212 ARG cc_start: 0.7347 (mmm160) cc_final: 0.7065 (mmm160) REVERT: D 275 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7432 (ttt-90) REVERT: E 27 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7268 (mt-10) REVERT: E 31 ILE cc_start: 0.8685 (mt) cc_final: 0.8209 (tt) REVERT: E 34 SER cc_start: 0.8282 (m) cc_final: 0.8064 (p) REVERT: E 36 HIS cc_start: 0.7668 (t70) cc_final: 0.7364 (t70) REVERT: E 47 MET cc_start: 0.8045 (mmm) cc_final: 0.7677 (tpp) REVERT: E 53 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8143 (ttm-80) REVERT: E 70 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8003 (ttmm) REVERT: E 90 SER cc_start: 0.8170 (t) cc_final: 0.7652 (p) REVERT: E 101 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7017 (mp0) REVERT: E 178 LEU cc_start: 0.8653 (tp) cc_final: 0.8403 (tt) REVERT: E 201 GLN cc_start: 0.8649 (mm110) cc_final: 0.8266 (mm-40) REVERT: E 202 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7657 (mmtm) REVERT: E 268 ILE cc_start: 0.8571 (mm) cc_final: 0.8154 (tp) REVERT: F 45 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8775 (ttmm) REVERT: F 48 GLN cc_start: 0.8221 (tt0) cc_final: 0.7736 (tt0) REVERT: F 70 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7202 (ttp80) REVERT: F 76 MET cc_start: 0.6767 (mmm) cc_final: 0.6505 (mmm) REVERT: F 101 VAL cc_start: 0.8598 (t) cc_final: 0.8259 (m) REVERT: F 134 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7392 (mm) REVERT: F 136 LEU cc_start: 0.8189 (mm) cc_final: 0.7906 (mt) REVERT: F 168 LEU cc_start: 0.8924 (tp) cc_final: 0.8717 (tp) REVERT: F 192 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7604 (mmmt) REVERT: F 202 LYS cc_start: 0.7856 (mttt) cc_final: 0.7428 (mttt) REVERT: F 225 LEU cc_start: 0.8446 (mt) cc_final: 0.8129 (mt) REVERT: F 226 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6980 (mm-30) REVERT: F 228 LEU cc_start: 0.8892 (mt) cc_final: 0.8493 (mt) REVERT: F 241 GLU cc_start: 0.6519 (tm-30) cc_final: 0.5655 (tm-30) REVERT: F 245 ILE cc_start: 0.8010 (mt) cc_final: 0.7425 (mt) REVERT: F 259 SER cc_start: 0.8269 (m) cc_final: 0.7875 (t) REVERT: F 283 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7184 (tm-30) REVERT: F 287 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6175 (ptp) REVERT: A 9 SER cc_start: 0.8806 (m) cc_final: 0.8405 (t) REVERT: A 131 GLU cc_start: 0.7565 (mp0) cc_final: 0.7351 (mp0) REVERT: A 136 CYS cc_start: 0.7002 (p) cc_final: 0.6686 (p) REVERT: A 165 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7810 (mmmt) REVERT: A 168 LEU cc_start: 0.8369 (mt) cc_final: 0.8107 (mt) REVERT: A 212 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7043 (mmm160) REVERT: B 31 ILE cc_start: 0.8730 (mt) cc_final: 0.8404 (mt) REVERT: B 34 SER cc_start: 0.8414 (m) cc_final: 0.8186 (p) REVERT: B 44 GLN cc_start: 0.8099 (mp10) cc_final: 0.7771 (mp10) REVERT: B 53 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8004 (ttm-80) REVERT: B 96 ARG cc_start: 0.7508 (pmt170) cc_final: 0.6681 (pmt170) REVERT: B 101 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6860 (mp0) REVERT: B 133 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: B 202 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7755 (mmtm) REVERT: B 243 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8134 (mmtm) REVERT: B 266 GLN cc_start: 0.8286 (tt0) cc_final: 0.8079 (tt0) REVERT: B 268 ILE cc_start: 0.8575 (mm) cc_final: 0.8066 (tp) REVERT: C 44 GLN cc_start: 0.8064 (tt0) cc_final: 0.7671 (tm-30) REVERT: C 48 GLN cc_start: 0.8193 (tt0) cc_final: 0.7721 (tm-30) REVERT: C 69 LYS cc_start: 0.8000 (tptm) cc_final: 0.7513 (tptt) REVERT: C 165 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7276 (mm) REVERT: C 171 PHE cc_start: 0.7864 (m-80) cc_final: 0.7587 (t80) REVERT: C 175 ASP cc_start: 0.7754 (p0) cc_final: 0.7141 (p0) REVERT: C 179 ARG cc_start: 0.7776 (mtm110) cc_final: 0.7254 (mtm110) REVERT: C 202 LYS cc_start: 0.8095 (mttt) cc_final: 0.7820 (mttt) REVERT: C 241 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5699 (tm-30) REVERT: C 263 TYR cc_start: 0.6866 (p90) cc_final: 0.6436 (p90) outliers start: 50 outliers final: 33 residues processed: 548 average time/residue: 0.1579 time to fit residues: 118.3059 Evaluate side-chains 574 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 536 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 115 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 HIS D 209 HIS D 246 GLN E 118 HIS E 133 GLN F 206 ASN A 133 GLN B 68 HIS B 177 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111294 restraints weight = 25589.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115120 restraints weight = 11676.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117527 restraints weight = 7035.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119015 restraints weight = 5094.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119847 restraints weight = 4176.223| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15692 Z= 0.137 Angle : 0.620 13.704 21696 Z= 0.315 Chirality : 0.042 0.252 2412 Planarity : 0.004 0.043 2466 Dihedral : 18.871 83.828 2758 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.50 % Allowed : 23.83 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.45 (0.21), residues: 1640 helix: 1.19 (0.19), residues: 766 sheet: 0.23 (0.33), residues: 200 loop : -0.66 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 204 TYR 0.013 0.001 TYR E 169 PHE 0.026 0.002 PHE C 141 TRP 0.016 0.001 TRP C 131 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00310 (15676) covalent geometry : angle 0.61900 (21688) hydrogen bonds : bond 0.03706 ( 655) hydrogen bonds : angle 4.52451 ( 1881) metal coordination : bond 0.01533 ( 16) metal coordination : angle 1.45065 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 550 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 GLN cc_start: 0.7396 (tp40) cc_final: 0.7090 (mp10) REVERT: D 142 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6445 (ptt-90) REVERT: D 165 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8009 (mmmt) REVERT: D 170 LYS cc_start: 0.8576 (mttt) cc_final: 0.7916 (mttt) REVERT: D 186 VAL cc_start: 0.8552 (t) cc_final: 0.8240 (p) REVERT: D 204 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8354 (mtt90) REVERT: D 212 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7161 (mmm160) REVERT: D 275 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7331 (ttt-90) REVERT: E 27 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7297 (mt-10) REVERT: E 31 ILE cc_start: 0.8681 (mt) cc_final: 0.8245 (mp) REVERT: E 34 SER cc_start: 0.8272 (m) cc_final: 0.8053 (p) REVERT: E 36 HIS cc_start: 0.7694 (t70) cc_final: 0.7378 (t70) REVERT: E 47 MET cc_start: 0.8068 (mmm) cc_final: 0.7688 (tpp) REVERT: E 49 ARG cc_start: 0.6967 (mtm180) cc_final: 0.6675 (mtm180) REVERT: E 53 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8164 (ttm-80) REVERT: E 70 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8019 (ttmm) REVERT: E 90 SER cc_start: 0.8164 (t) cc_final: 0.7635 (p) REVERT: E 101 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6999 (mp0) REVERT: E 158 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7348 (mm-30) REVERT: E 178 LEU cc_start: 0.8638 (tp) cc_final: 0.8403 (tt) REVERT: E 201 GLN cc_start: 0.8634 (mm110) cc_final: 0.8248 (mm-40) REVERT: E 202 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7635 (mmtm) REVERT: E 268 ILE cc_start: 0.8573 (mm) cc_final: 0.8142 (tp) REVERT: F 45 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8643 (ttmm) REVERT: F 48 GLN cc_start: 0.8232 (tt0) cc_final: 0.7785 (tt0) REVERT: F 69 LYS cc_start: 0.8302 (tttt) cc_final: 0.7872 (tttp) REVERT: F 70 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7194 (ttp80) REVERT: F 76 MET cc_start: 0.6824 (mmm) cc_final: 0.6565 (mmm) REVERT: F 83 ASN cc_start: 0.8110 (m-40) cc_final: 0.7579 (m-40) REVERT: F 101 VAL cc_start: 0.8569 (t) cc_final: 0.8237 (m) REVERT: F 134 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7394 (mm) REVERT: F 192 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7597 (mmmt) REVERT: F 202 LYS cc_start: 0.7890 (mttt) cc_final: 0.7466 (mttt) REVERT: F 225 LEU cc_start: 0.8455 (mt) cc_final: 0.8106 (mt) REVERT: F 226 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6973 (mm-30) REVERT: F 228 LEU cc_start: 0.8914 (mt) cc_final: 0.8661 (mm) REVERT: F 241 GLU cc_start: 0.6527 (tm-30) cc_final: 0.5642 (tm-30) REVERT: F 245 ILE cc_start: 0.7992 (mt) cc_final: 0.7418 (mt) REVERT: F 259 SER cc_start: 0.8247 (m) cc_final: 0.7871 (t) REVERT: F 283 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7086 (tm-30) REVERT: F 287 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6005 (ptp) REVERT: A 9 SER cc_start: 0.8822 (m) cc_final: 0.8412 (t) REVERT: A 131 GLU cc_start: 0.7611 (mp0) cc_final: 0.7389 (mp0) REVERT: A 136 CYS cc_start: 0.6970 (p) cc_final: 0.6667 (p) REVERT: A 165 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7875 (mmmt) REVERT: A 168 LEU cc_start: 0.8357 (mt) cc_final: 0.8118 (mt) REVERT: A 204 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8198 (mtt90) REVERT: A 212 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7057 (mmm160) REVERT: B 31 ILE cc_start: 0.8725 (mt) cc_final: 0.8383 (mt) REVERT: B 34 SER cc_start: 0.8416 (m) cc_final: 0.8200 (p) REVERT: B 44 GLN cc_start: 0.8101 (mp10) cc_final: 0.7816 (mp10) REVERT: B 53 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8004 (ttm-80) REVERT: B 72 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8134 (mttp) REVERT: B 96 ARG cc_start: 0.7530 (pmt170) cc_final: 0.6964 (pmt170) REVERT: B 101 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6846 (mp0) REVERT: B 133 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: B 158 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 202 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7708 (mmtm) REVERT: B 243 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8117 (mmtm) REVERT: B 268 ILE cc_start: 0.8570 (mm) cc_final: 0.8075 (tp) REVERT: C 44 GLN cc_start: 0.8004 (tt0) cc_final: 0.7608 (tm-30) REVERT: C 48 GLN cc_start: 0.8253 (tt0) cc_final: 0.7716 (tm-30) REVERT: C 69 LYS cc_start: 0.7962 (tptm) cc_final: 0.7534 (tppt) REVERT: C 79 TYR cc_start: 0.6893 (t80) cc_final: 0.6300 (t80) REVERT: C 103 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6329 (mmm) REVERT: C 134 LEU cc_start: 0.7671 (mm) cc_final: 0.7235 (mm) REVERT: C 165 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7324 (mm) REVERT: C 171 PHE cc_start: 0.7887 (m-80) cc_final: 0.7561 (t80) REVERT: C 175 ASP cc_start: 0.7672 (p0) cc_final: 0.7066 (p0) REVERT: C 179 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7207 (mtm110) REVERT: C 202 LYS cc_start: 0.8063 (mttt) cc_final: 0.7795 (mttt) REVERT: C 241 GLU cc_start: 0.6381 (tm-30) cc_final: 0.5717 (tm-30) REVERT: C 263 TYR cc_start: 0.6889 (p90) cc_final: 0.6436 (p90) REVERT: C 292 TYR cc_start: 0.7480 (m-80) cc_final: 0.7035 (m-80) outliers start: 51 outliers final: 37 residues processed: 567 average time/residue: 0.1496 time to fit residues: 117.1779 Evaluate side-chains 592 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 548 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 HIS D 209 HIS D 250 GLN E 118 HIS E 133 GLN E 201 GLN F 206 ASN B 68 HIS B 123 ASN B 266 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111763 restraints weight = 25621.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115534 restraints weight = 11658.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117891 restraints weight = 7030.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119354 restraints weight = 5119.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120244 restraints weight = 4223.048| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15692 Z= 0.170 Angle : 0.632 11.821 21696 Z= 0.324 Chirality : 0.043 0.269 2412 Planarity : 0.004 0.062 2466 Dihedral : 18.884 83.270 2758 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.57 % Allowed : 23.63 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.38 (0.21), residues: 1640 helix: 1.10 (0.19), residues: 774 sheet: 0.17 (0.33), residues: 200 loop : -0.67 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 177 TYR 0.014 0.001 TYR E 169 PHE 0.031 0.002 PHE F 163 TRP 0.021 0.001 TRP C 131 HIS 0.016 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00378 (15676) covalent geometry : angle 0.62988 (21688) hydrogen bonds : bond 0.03849 ( 655) hydrogen bonds : angle 4.55937 ( 1881) metal coordination : bond 0.02376 ( 16) metal coordination : angle 2.50367 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 543 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7346 (ptpp) cc_final: 0.6914 (ptpp) REVERT: D 133 GLN cc_start: 0.7353 (tp40) cc_final: 0.7050 (mp10) REVERT: D 165 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7958 (mmmt) REVERT: D 170 LYS cc_start: 0.8589 (mttt) cc_final: 0.7943 (mttt) REVERT: D 186 VAL cc_start: 0.8579 (t) cc_final: 0.8284 (p) REVERT: D 204 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8344 (mtt90) REVERT: D 212 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7172 (mmm160) REVERT: D 275 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7412 (ttt-90) REVERT: E 27 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7257 (mt-10) REVERT: E 31 ILE cc_start: 0.8699 (mt) cc_final: 0.8279 (mp) REVERT: E 34 SER cc_start: 0.8271 (m) cc_final: 0.8070 (p) REVERT: E 36 HIS cc_start: 0.7654 (t70) cc_final: 0.7144 (t70) REVERT: E 40 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7824 (mtmm) REVERT: E 47 MET cc_start: 0.8034 (mmm) cc_final: 0.7676 (tpp) REVERT: E 49 ARG cc_start: 0.6908 (mtm180) cc_final: 0.6623 (mtm180) REVERT: E 53 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8163 (ttm-80) REVERT: E 70 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7988 (ttmm) REVERT: E 90 SER cc_start: 0.8169 (t) cc_final: 0.7665 (p) REVERT: E 101 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7012 (mp0) REVERT: E 178 LEU cc_start: 0.8666 (tp) cc_final: 0.8455 (tt) REVERT: E 201 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8276 (mm-40) REVERT: E 202 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7700 (mmtm) REVERT: E 268 ILE cc_start: 0.8590 (mm) cc_final: 0.8171 (tp) REVERT: F 45 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8710 (ttmm) REVERT: F 48 GLN cc_start: 0.8207 (tt0) cc_final: 0.7763 (tt0) REVERT: F 70 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7175 (ttp80) REVERT: F 76 MET cc_start: 0.6782 (mmm) cc_final: 0.6495 (mmm) REVERT: F 83 ASN cc_start: 0.8080 (m-40) cc_final: 0.7551 (m-40) REVERT: F 101 VAL cc_start: 0.8525 (t) cc_final: 0.8206 (m) REVERT: F 192 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7504 (mmmt) REVERT: F 202 LYS cc_start: 0.7973 (mttt) cc_final: 0.7536 (mttt) REVERT: F 225 LEU cc_start: 0.8422 (mt) cc_final: 0.8043 (mt) REVERT: F 226 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6957 (mm-30) REVERT: F 228 LEU cc_start: 0.8930 (mt) cc_final: 0.8690 (mm) REVERT: F 241 GLU cc_start: 0.6540 (tm-30) cc_final: 0.5616 (tm-30) REVERT: F 245 ILE cc_start: 0.7963 (mt) cc_final: 0.7383 (mt) REVERT: F 259 SER cc_start: 0.8307 (m) cc_final: 0.7908 (t) REVERT: F 283 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7088 (tm-30) REVERT: F 287 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5995 (ptp) REVERT: A 9 SER cc_start: 0.8828 (m) cc_final: 0.8405 (p) REVERT: A 131 GLU cc_start: 0.7542 (mp0) cc_final: 0.7307 (mp0) REVERT: A 136 CYS cc_start: 0.6958 (p) cc_final: 0.6634 (p) REVERT: A 165 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7850 (mmmt) REVERT: A 204 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8170 (mtt90) REVERT: A 212 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7064 (mmm160) REVERT: B 31 ILE cc_start: 0.8751 (mt) cc_final: 0.8412 (mt) REVERT: B 34 SER cc_start: 0.8419 (m) cc_final: 0.8215 (p) REVERT: B 53 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8002 (ttm-80) REVERT: B 72 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: B 96 ARG cc_start: 0.7528 (pmt170) cc_final: 0.6833 (pmt170) REVERT: B 101 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6878 (mp0) REVERT: B 133 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: B 201 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8222 (mm110) REVERT: B 202 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7618 (mmtm) REVERT: B 243 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8160 (mmtm) REVERT: B 268 ILE cc_start: 0.8567 (mm) cc_final: 0.8117 (tp) REVERT: C 44 GLN cc_start: 0.8058 (tt0) cc_final: 0.7593 (tm-30) REVERT: C 69 LYS cc_start: 0.8024 (tptm) cc_final: 0.7561 (tptt) REVERT: C 79 TYR cc_start: 0.6898 (t80) cc_final: 0.6328 (t80) REVERT: C 103 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6382 (mmm) REVERT: C 134 LEU cc_start: 0.7713 (mm) cc_final: 0.7313 (mm) REVERT: C 165 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7338 (mm) REVERT: C 171 PHE cc_start: 0.7810 (m-80) cc_final: 0.7583 (t80) REVERT: C 175 ASP cc_start: 0.7741 (p0) cc_final: 0.7080 (p0) REVERT: C 179 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7223 (mtm110) REVERT: C 202 LYS cc_start: 0.8091 (mttt) cc_final: 0.7827 (mttt) REVERT: C 241 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5667 (tm-30) REVERT: C 263 TYR cc_start: 0.6865 (p90) cc_final: 0.6425 (p90) REVERT: C 292 TYR cc_start: 0.7450 (m-80) cc_final: 0.7015 (m-80) REVERT: C 306 ASN cc_start: 0.7382 (m-40) cc_final: 0.7163 (m-40) outliers start: 52 outliers final: 37 residues processed: 562 average time/residue: 0.1541 time to fit residues: 119.2843 Evaluate side-chains 591 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 549 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 126 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 HIS D 209 HIS D 250 GLN E 118 HIS E 133 GLN F 206 ASN B 68 HIS B 123 ASN B 177 ASN C 166 GLN C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112283 restraints weight = 25724.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116054 restraints weight = 11677.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118428 restraints weight = 7023.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119907 restraints weight = 5107.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120799 restraints weight = 4220.709| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15692 Z= 0.150 Angle : 0.652 13.959 21696 Z= 0.332 Chirality : 0.043 0.252 2412 Planarity : 0.004 0.059 2466 Dihedral : 18.860 83.092 2758 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.23 % Allowed : 24.04 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.40 (0.21), residues: 1640 helix: 1.10 (0.19), residues: 774 sheet: 0.17 (0.34), residues: 200 loop : -0.63 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 177 TYR 0.014 0.001 TYR E 169 PHE 0.029 0.002 PHE F 163 TRP 0.021 0.001 TRP C 131 HIS 0.022 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00341 (15676) covalent geometry : angle 0.65087 (21688) hydrogen bonds : bond 0.03752 ( 655) hydrogen bonds : angle 4.53532 ( 1881) metal coordination : bond 0.01841 ( 16) metal coordination : angle 1.79043 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 549 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7339 (ptpp) cc_final: 0.6909 (ptpp) REVERT: D 133 GLN cc_start: 0.7327 (tp40) cc_final: 0.7032 (mp10) REVERT: D 165 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7935 (mmmt) REVERT: D 170 LYS cc_start: 0.8587 (mttt) cc_final: 0.7920 (mttt) REVERT: D 186 VAL cc_start: 0.8572 (t) cc_final: 0.8276 (p) REVERT: D 212 ARG cc_start: 0.7477 (mmm160) cc_final: 0.7151 (mmm160) REVERT: D 275 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7402 (ttt-90) REVERT: E 27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7242 (mt-10) REVERT: E 31 ILE cc_start: 0.8695 (mt) cc_final: 0.8260 (mp) REVERT: E 34 SER cc_start: 0.8258 (m) cc_final: 0.8057 (p) REVERT: E 36 HIS cc_start: 0.7643 (t70) cc_final: 0.7104 (t70) REVERT: E 40 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7827 (mtmm) REVERT: E 47 MET cc_start: 0.8037 (mmm) cc_final: 0.7690 (tpp) REVERT: E 49 ARG cc_start: 0.6906 (mtm180) cc_final: 0.6614 (mtm180) REVERT: E 53 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8155 (ttm-80) REVERT: E 70 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7980 (ttmm) REVERT: E 90 SER cc_start: 0.8154 (t) cc_final: 0.7644 (p) REVERT: E 101 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6986 (mp0) REVERT: E 120 ASN cc_start: 0.8170 (p0) cc_final: 0.7884 (p0) REVERT: E 178 LEU cc_start: 0.8669 (tp) cc_final: 0.8468 (tt) REVERT: E 201 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8160 (mm-40) REVERT: E 202 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7682 (mmtm) REVERT: E 268 ILE cc_start: 0.8590 (mm) cc_final: 0.8167 (tp) REVERT: F 45 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8785 (ttmm) REVERT: F 48 GLN cc_start: 0.8205 (tt0) cc_final: 0.7739 (tt0) REVERT: F 70 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7183 (ttp80) REVERT: F 76 MET cc_start: 0.6742 (mmm) cc_final: 0.6477 (mmm) REVERT: F 83 ASN cc_start: 0.8078 (m-40) cc_final: 0.7541 (m-40) REVERT: F 91 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7593 (mt) REVERT: F 101 VAL cc_start: 0.8493 (t) cc_final: 0.8179 (m) REVERT: F 136 LEU cc_start: 0.8188 (mm) cc_final: 0.7933 (mt) REVERT: F 192 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7504 (mmmt) REVERT: F 202 LYS cc_start: 0.7980 (mttt) cc_final: 0.7537 (mttt) REVERT: F 225 LEU cc_start: 0.8433 (mt) cc_final: 0.8093 (mt) REVERT: F 226 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6969 (mm-30) REVERT: F 228 LEU cc_start: 0.8948 (mt) cc_final: 0.8712 (mm) REVERT: F 241 GLU cc_start: 0.6536 (tm-30) cc_final: 0.5614 (tm-30) REVERT: F 245 ILE cc_start: 0.7980 (mt) cc_final: 0.7387 (mt) REVERT: F 259 SER cc_start: 0.8298 (m) cc_final: 0.7904 (t) REVERT: F 283 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7066 (tm-30) REVERT: F 287 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5978 (ptp) REVERT: A 9 SER cc_start: 0.8829 (m) cc_final: 0.8374 (p) REVERT: A 131 GLU cc_start: 0.7547 (mp0) cc_final: 0.7307 (mp0) REVERT: A 136 CYS cc_start: 0.6967 (p) cc_final: 0.6642 (p) REVERT: A 165 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7845 (mmmt) REVERT: A 212 ARG cc_start: 0.7520 (mmm160) cc_final: 0.7063 (mmm160) REVERT: B 31 ILE cc_start: 0.8754 (mt) cc_final: 0.8415 (mt) REVERT: B 34 SER cc_start: 0.8416 (m) cc_final: 0.8207 (p) REVERT: B 72 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: B 133 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: B 158 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 202 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7758 (mmtm) REVERT: B 243 LYS cc_start: 0.8401 (mmtp) cc_final: 0.8160 (mmtm) REVERT: B 268 ILE cc_start: 0.8592 (mm) cc_final: 0.8104 (tp) REVERT: C 69 LYS cc_start: 0.7993 (tptm) cc_final: 0.7619 (tptt) REVERT: C 79 TYR cc_start: 0.6889 (t80) cc_final: 0.6396 (t80) REVERT: C 134 LEU cc_start: 0.7777 (mm) cc_final: 0.7448 (mm) REVERT: C 165 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7360 (mm) REVERT: C 166 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: C 175 ASP cc_start: 0.7698 (p0) cc_final: 0.7018 (p0) REVERT: C 179 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7112 (mtm110) REVERT: C 202 LYS cc_start: 0.8090 (mttt) cc_final: 0.7833 (mttt) REVERT: C 210 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7324 (mpp80) REVERT: C 241 GLU cc_start: 0.6364 (tm-30) cc_final: 0.5602 (tm-30) REVERT: C 263 TYR cc_start: 0.6899 (p90) cc_final: 0.6445 (p90) REVERT: C 292 TYR cc_start: 0.7478 (m-80) cc_final: 0.7026 (m-80) REVERT: C 306 ASN cc_start: 0.7295 (m-40) cc_final: 0.7086 (m-40) outliers start: 47 outliers final: 34 residues processed: 567 average time/residue: 0.1624 time to fit residues: 126.4248 Evaluate side-chains 587 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 547 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.0270 chunk 149 optimal weight: 0.0070 chunk 108 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 HIS D 250 GLN ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 133 GLN E 195 ASN B 68 HIS B 201 GLN B 266 GLN C 166 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112473 restraints weight = 25540.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116260 restraints weight = 11626.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118620 restraints weight = 6993.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120100 restraints weight = 5090.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120972 restraints weight = 4194.375| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 15692 Z= 0.228 Angle : 0.865 59.200 21696 Z= 0.485 Chirality : 0.049 1.045 2412 Planarity : 0.005 0.166 2466 Dihedral : 18.865 83.088 2758 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 24.73 % Favored : 72.53 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.51 % 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: 0.40 (0.21), residues: 1640 helix: 1.09 (0.19), residues: 774 sheet: 0.18 (0.34), residues: 200 loop : -0.62 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 143 TYR 0.037 0.002 TYR F 158 PHE 0.027 0.002 PHE C 150 TRP 0.017 0.001 TRP C 131 HIS 0.016 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00466 (15676) covalent geometry : angle 0.86404 (21688) hydrogen bonds : bond 0.03792 ( 655) hydrogen bonds : angle 4.53447 ( 1881) metal coordination : bond 0.01821 ( 16) metal coordination : angle 1.78041 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.43 seconds wall clock time: 59 minutes 22.81 seconds (3562.81 seconds total)