Starting phenix.real_space_refine on Sat Sep 12 09:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ouh_13077/09_2026/7ouh_13077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ouh_13077/09_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_13077/09_2026/7ouh_13077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ouh_13077/09_2026/7ouh_13077.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ouh_13077/09_2026/7ouh_13077.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ouh_13077/09_2026/7ouh_13077.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ouh_13077/09_2026/7ouh_13077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ouh_13077/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.84, per 1000 atoms: 0.32 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: 1.24 Conformation dependent library (CDL) restraints added in 767.6 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: 1.63 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: 2.52 Time building geometry restraints manager: 1.67 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: 2017 0.053 - 0.106: 347 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: 0.03 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: 2.850 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.870 Find NCS groups from input model: 0.130 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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= 0.392 Angle : 0.820 42.568 21696 Z= 0.410 Chirality : 0.042 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/Z covalent geometry : bond 0.00696 / 0.39 (15676) covalent geometry : angle 0.66864 / 0.40 (21688) hydrogen bonds : bond 0.17985 / 12.80 ( 655) hydrogen bonds : angle 6.48232 / 4.59 ( 1881) metal coordination : bond 0.01010 / 0.59 ( 16) metal coordination : angle 24.69507 / 12.37 ( 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 : 0.435 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: 0.7484 (tt) REVERT: D 36 HIS cc_start: 0.6613 (t70) cc_final: 0.6273 (t70) REVERT: D 165 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6826 (mmmt) REVERT: D 167 LEU cc_start: 0.8451 (mt) cc_final: 0.8060 (mt) REVERT: E 26 THR cc_start: 0.8081 (p) cc_final: 0.7745 (p) REVERT: E 39 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7664 (mmm160) REVERT: E 53 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7974 (ttm-80) REVERT: E 90 SER cc_start: 0.8020 (t) cc_final: 0.7725 (p) REVERT: E 164 LEU cc_start: 0.8516 (tp) cc_final: 0.8283 (tp) REVERT: E 172 PHE cc_start: 0.8457 (m-10) cc_final: 0.8206 (m-80) REVERT: F 32 ASP cc_start: 0.6853 (m-30) cc_final: 0.6590 (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: 0.5903 (tt) REVERT: F 168 LEU cc_start: 0.8188 (tp) cc_final: 0.7883 (tp) REVERT: F 228 LEU cc_start: 0.8312 (mt) cc_final: 0.8027 (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: 0.7121 (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: 0.7220 (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: 0.6949 (mt) REVERT: A 200 CYS cc_start: 0.6948 (p) cc_final: 0.6707 (p) REVERT: B 99 SER cc_start: 0.7288 (m) cc_final: 0.6960 (p) REVERT: B 130 GLN cc_start: 0.6414 (tp-100) cc_final: 0.6183 (tp-100) REVERT: B 150 ASN cc_start: 0.8088 (t0) cc_final: 0.7857 (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: 0.6970 (m-30) REVERT: C 196 LEU cc_start: 0.7562 (mp) cc_final: 0.7322 (mt) REVERT: C 204 ILE cc_start: 0.8413 (tp) cc_final: 0.7681 (tp) REVERT: C 208 PHE cc_start: 0.6614 (m-10) cc_final: 0.6337 (m-80) REVERT: C 256 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7643 (ptpt) REVERT: C 263 TYR cc_start: 0.5717 (p90) cc_final: 0.5334 (p90) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.1426 time to fit residues: 111.2066 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 : 0.528 ------------------------------------------------------------------------------- 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: 3.9990 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... E 123 ASN E 195 ASN E 201 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN B 41 ASN B 192 ASN B 195 ASN B 201 GLN 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 = 0.3859 r_free = 0.3859 target = 0.140057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110580 restraints weight = 26300.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114264 restraints weight = 12163.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116553 restraints weight = 7307.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117985 restraints weight = 5293.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118863 restraints weight = 4350.922| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2002 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= 0.201 Angle : 0.660 8.148 21696 Z= 0.347 Chirality : 0.045 0.217 2412 Planarity : 0.005 0.076 2466 Dihedral : 18.861 82.581 2758 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 11.26 % Favored : 86.74 % 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: 0.29 (0.21), residues: 1640 helix: 0.98 (0.19), residues: 768 sheet: 0.19 (0.32), residues: 220 loop : -0.68 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 204 TYR 0.023 0.002 TYR F 263 PHE 0.027 0.002 PHE F 246 TRP 0.007 0.001 TRP D 242 HIS 0.014 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (15676) covalent geometry : angle 0.65701 / 0.35 (21688) hydrogen bonds : bond 0.05542 / 3.82 ( 655) hydrogen bonds : angle 5.06389 / 3.62 ( 1881) metal coordination : bond 0.03354 / 1.85 ( 16) metal coordination : angle 3.38996 / 1.86 ( 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 553 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 524 time to evaluate : 0.388 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 165 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7975 (mmmt) REVERT: D 167 LEU cc_start: 0.8428 (mt) cc_final: 0.8132 (mt) REVERT: D 216 ILE cc_start: 0.7980 (mt) cc_final: 0.7264 (mp) REVERT: D 232 PHE cc_start: 0.8097 (p90) cc_final: 0.7864 (p90) REVERT: D 273 LEU cc_start: 0.8457 (mt) cc_final: 0.8162 (mm) REVERT: E 27 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 33 HIS cc_start: 0.7500 (m-70) cc_final: 0.7255 (m-70) REVERT: E 36 HIS cc_start: 0.7701 (t70) cc_final: 0.7383 (t-90) REVERT: E 53 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8224 (ttm-80) REVERT: E 90 SER cc_start: 0.8206 (t) cc_final: 0.7713 (p) REVERT: E 101 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7007 (mp0) REVERT: E 172 PHE cc_start: 0.8875 (m-10) cc_final: 0.8620 (m-80) REVERT: E 202 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7795 (mttm) REVERT: E 232 PHE cc_start: 0.8143 (p90) cc_final: 0.7762 (p90) REVERT: F 47 ARG cc_start: 0.7282 (mtp180) cc_final: 0.6997 (mtp-110) REVERT: F 67 GLU cc_start: 0.7588 (tp30) cc_final: 0.6779 (tp30) REVERT: F 70 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7462 (ttp80) REVERT: F 93 PRO cc_start: 0.7596 (Cg_exo) cc_final: 0.7343 (Cg_endo) REVERT: F 149 ASP cc_start: 0.7048 (m-30) cc_final: 0.6799 (m-30) REVERT: F 159 ILE cc_start: 0.7069 (mm) cc_final: 0.6785 (mt) REVERT: F 168 LEU cc_start: 0.8722 (tp) cc_final: 0.8341 (tp) REVERT: F 202 LYS cc_start: 0.7373 (mttt) cc_final: 0.7018 (mttt) REVERT: F 203 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8168 (tm-30) REVERT: F 211 PHE cc_start: 0.8390 (t80) cc_final: 0.8153 (t80) REVERT: F 225 LEU cc_start: 0.8371 (mt) cc_final: 0.8098 (mt) REVERT: F 226 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7007 (mm-30) REVERT: F 228 LEU cc_start: 0.8813 (mt) cc_final: 0.8461 (mt) REVERT: F 241 GLU cc_start: 0.6254 (tm-30) cc_final: 0.5600 (tm-30) REVERT: F 245 ILE cc_start: 0.8214 (mt) cc_final: 0.7742 (mt) REVERT: F 256 LYS cc_start: 0.7852 (ptpt) cc_final: 0.7287 (ptpt) REVERT: F 283 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7630 (tm-30) REVERT: F 287 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6352 (ptp) REVERT: F 301 GLU cc_start: 0.6695 (mm-30) cc_final: 0.5788 (mm-30) REVERT: A 54 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7357 (mmm160) REVERT: A 165 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7643 (mmmt) REVERT: A 170 LYS cc_start: 0.8400 (mttt) cc_final: 0.8182 (mttt) REVERT: A 172 PHE cc_start: 0.8128 (m-80) cc_final: 0.7907 (m-80) REVERT: A 212 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7164 (mmm160) REVERT: B 31 ILE cc_start: 0.8775 (mt) cc_final: 0.8352 (tt) REVERT: B 34 SER cc_start: 0.8385 (m) cc_final: 0.8136 (p) REVERT: B 47 MET cc_start: 0.7629 (mmm) cc_final: 0.7330 (mmm) REVERT: B 70 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7908 (ttmm) REVERT: B 93 HIS cc_start: 0.8299 (p-80) cc_final: 0.8091 (p90) REVERT: B 133 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: B 171 TYR cc_start: 0.8818 (m-10) cc_final: 0.8547 (m-10) REVERT: B 202 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7746 (mttm) REVERT: B 266 GLN cc_start: 0.8220 (tt0) cc_final: 0.7950 (tt0) REVERT: C 44 GLN cc_start: 0.7960 (tt0) cc_final: 0.7637 (tm-30) REVERT: C 97 HIS cc_start: 0.7735 (t-90) cc_final: 0.7524 (t-90) REVERT: C 134 LEU cc_start: 0.7767 (mp) cc_final: 0.7521 (mm) REVERT: C 171 PHE cc_start: 0.7902 (m-80) cc_final: 0.7596 (t80) REVERT: C 177 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7384 (mpp80) REVERT: C 181 PHE cc_start: 0.8741 (m-80) cc_final: 0.8523 (m-10) REVERT: C 202 LYS cc_start: 0.7768 (mttt) cc_final: 0.7553 (mttt) REVERT: C 204 ILE cc_start: 0.8457 (tp) cc_final: 0.8126 (tp) REVERT: C 206 ASN cc_start: 0.6876 (t0) cc_final: 0.6579 (t0) REVERT: C 241 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5742 (tm-30) REVERT: C 263 TYR cc_start: 0.6451 (p90) cc_final: 0.6093 (p90) outliers start: 29 outliers final: 21 residues processed: 532 average time/residue: 0.1453 time to fit residues: 107.6875 Evaluate side-chains 532 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 509 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 ASN 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 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: 8.9990 chunk 137 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 139 optimal weight: 0.0030 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 175 ASN F 44 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS A 161 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 79 HIS B 123 ASN B 130 GLN B 201 GLN B 208 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110689 restraints weight = 26002.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114509 restraints weight = 11997.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116861 restraints weight = 7247.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118361 restraints weight = 5288.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119260 restraints weight = 4347.508| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15692 Z= 0.218 Angle : 0.644 11.135 21696 Z= 0.336 Chirality : 0.045 0.265 2412 Planarity : 0.005 0.068 2466 Dihedral : 19.078 84.044 2758 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.88 % Allowed : 15.52 % Favored : 81.59 % 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: 0.12 (0.20), residues: 1640 helix: 0.89 (0.19), residues: 764 sheet: 0.13 (0.32), residues: 220 loop : -0.84 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 115 TYR 0.023 0.002 TYR C 158 PHE 0.026 0.002 PHE C 150 TRP 0.012 0.002 TRP B 205 HIS 0.014 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (15676) covalent geometry : angle 0.63714 / 0.34 (21688) hydrogen bonds : bond 0.05212 / 3.60 ( 655) hydrogen bonds : angle 4.90772 / 3.50 ( 1881) metal coordination : bond 0.03215 / 1.76 ( 16) metal coordination : angle 5.07018 / 2.52 ( 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 575 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 533 time to evaluate : 0.447 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: 0.8342 (mmmt) cc_final: 0.8021 (mmmt) REVERT: D 167 LEU cc_start: 0.8432 (mt) cc_final: 0.8224 (mt) REVERT: D 170 LYS cc_start: 0.8493 (mttt) cc_final: 0.7899 (mttt) REVERT: D 186 VAL cc_start: 0.8525 (t) cc_final: 0.8252 (p) REVERT: D 192 ASN cc_start: 0.8897 (m-40) cc_final: 0.8682 (m-40) REVERT: D 212 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7045 (mmm160) REVERT: D 216 ILE cc_start: 0.7793 (mt) cc_final: 0.7255 (mm) REVERT: D 233 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8478 (mtmm) REVERT: D 273 LEU cc_start: 0.8483 (mt) cc_final: 0.8190 (mm) REVERT: E 27 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 36 HIS cc_start: 0.7744 (t70) cc_final: 0.7502 (t70) REVERT: E 53 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8198 (ttm-80) REVERT: E 90 SER cc_start: 0.8221 (t) cc_final: 0.7709 (p) REVERT: E 101 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6958 (mp0) REVERT: E 202 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7833 (mmtm) REVERT: E 232 PHE cc_start: 0.8186 (p90) cc_final: 0.7797 (p90) REVERT: F 47 ARG cc_start: 0.7324 (mtp180) cc_final: 0.7028 (mtp-110) REVERT: F 48 GLN cc_start: 0.8187 (tt0) cc_final: 0.7697 (tt0) REVERT: F 67 GLU cc_start: 0.7660 (tp30) cc_final: 0.6931 (tp30) REVERT: F 101 VAL cc_start: 0.8555 (t) cc_final: 0.8237 (m) REVERT: F 134 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7442 (mm) REVERT: F 149 ASP cc_start: 0.7100 (m-30) cc_final: 0.6870 (m-30) REVERT: F 159 ILE cc_start: 0.7087 (mm) cc_final: 0.6450 (tt) REVERT: F 168 LEU cc_start: 0.8809 (tp) cc_final: 0.8464 (tp) REVERT: F 171 PHE cc_start: 0.8244 (t80) cc_final: 0.7900 (t80) REVERT: F 202 LYS cc_start: 0.7490 (mttt) cc_final: 0.7100 (mttt) REVERT: F 211 PHE cc_start: 0.8380 (t80) cc_final: 0.8172 (t80) REVERT: F 226 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6915 (mm-30) REVERT: F 228 LEU cc_start: 0.8849 (mt) cc_final: 0.8507 (mt) REVERT: F 241 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5708 (tm-30) REVERT: F 245 ILE cc_start: 0.8009 (mt) cc_final: 0.7499 (mt) REVERT: F 256 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7325 (ptpt) REVERT: F 259 SER cc_start: 0.8286 (m) cc_final: 0.7990 (t) REVERT: F 301 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 7 LEU cc_start: 0.8388 (tp) cc_final: 0.8154 (tt) REVERT: A 165 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7733 (mmmt) REVERT: A 170 LYS cc_start: 0.8449 (mttt) cc_final: 0.8174 (mttt) REVERT: A 172 PHE cc_start: 0.8163 (m-80) cc_final: 0.7952 (m-80) REVERT: A 202 LYS cc_start: 0.7964 (mttt) cc_final: 0.7764 (mtpp) REVERT: A 212 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7135 (mmm160) REVERT: B 27 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 31 ILE cc_start: 0.8738 (mt) cc_final: 0.8388 (mp) REVERT: B 34 SER cc_start: 0.8426 (m) cc_final: 0.8182 (p) REVERT: B 131 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6889 (mp0) REVERT: B 202 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7736 (mmtm) REVERT: B 266 GLN cc_start: 0.8320 (tt0) cc_final: 0.8090 (tt0) REVERT: C 44 GLN cc_start: 0.7996 (tt0) cc_final: 0.7669 (tm-30) REVERT: C 48 GLN cc_start: 0.8184 (tt0) cc_final: 0.7681 (tt0) REVERT: C 69 LYS cc_start: 0.8129 (tptm) cc_final: 0.7329 (tptt) REVERT: C 101 VAL cc_start: 0.8291 (t) cc_final: 0.8047 (m) REVERT: C 158 TYR cc_start: 0.6539 (m-10) cc_final: 0.6305 (m-10) REVERT: C 165 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7323 (mm) REVERT: C 171 PHE cc_start: 0.8067 (m-80) cc_final: 0.7709 (t80) REVERT: C 177 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7522 (mtm180) REVERT: C 202 LYS cc_start: 0.7825 (mttt) cc_final: 0.7571 (mttt) REVERT: C 204 ILE cc_start: 0.8466 (tp) cc_final: 0.8226 (tp) REVERT: C 206 ASN cc_start: 0.7128 (t0) cc_final: 0.6805 (t0) REVERT: C 241 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5725 (tm-30) REVERT: C 263 TYR cc_start: 0.6653 (p90) cc_final: 0.6271 (p90) REVERT: C 287 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6244 (ppp) REVERT: C 305 LEU cc_start: 0.7985 (mm) cc_final: 0.7768 (mm) outliers start: 42 outliers final: 29 residues processed: 543 average time/residue: 0.1478 time to fit residues: 111.1136 Evaluate side-chains 534 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 502 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 152 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 246 PHE 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 136 CYS Chi-restraints excluded: chain A residue 196 VAL 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 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 95 VAL Chi-restraints excluded: chain C residue 98 MET 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 232 ILE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 193 HIS D 209 HIS E 30 ASN E 33 HIS A 209 HIS B 123 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110888 restraints weight = 25914.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114671 restraints weight = 12049.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117046 restraints weight = 7309.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118515 restraints weight = 5322.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119407 restraints weight = 4385.818| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15692 Z= 0.195 Angle : 0.624 8.770 21696 Z= 0.326 Chirality : 0.043 0.246 2412 Planarity : 0.005 0.053 2466 Dihedral : 19.148 85.552 2758 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.05 % Allowed : 17.72 % Favored : 78.23 % 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: 0.13 (0.20), residues: 1640 helix: 0.89 (0.19), residues: 772 sheet: 0.15 (0.32), residues: 220 loop : -0.84 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 115 TYR 0.015 0.002 TYR E 169 PHE 0.029 0.002 PHE C 150 TRP 0.012 0.001 TRP B 205 HIS 0.008 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (15676) covalent geometry : angle 0.61891 / 0.33 (21688) hydrogen bonds : bond 0.04711 / 3.26 ( 655) hydrogen bonds : angle 4.79397 / 3.41 ( 1881) metal coordination : bond 0.02855 / 1.57 ( 16) metal coordination : angle 3.99305 / 1.96 ( 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 582 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 523 time to evaluate : 0.372 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: D 165 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8043 (mmmt) REVERT: D 170 LYS cc_start: 0.8506 (mttt) cc_final: 0.8180 (mttt) REVERT: D 186 VAL cc_start: 0.8569 (t) cc_final: 0.8235 (p) REVERT: D 212 ARG cc_start: 0.7387 (mmm160) cc_final: 0.7053 (mmm160) REVERT: D 233 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8466 (mtmm) REVERT: D 273 LEU cc_start: 0.8541 (mt) cc_final: 0.8322 (mm) REVERT: E 31 ILE cc_start: 0.8691 (mp) cc_final: 0.8385 (mp) REVERT: E 34 SER cc_start: 0.8320 (m) cc_final: 0.8034 (p) REVERT: E 36 HIS cc_start: 0.7729 (t70) cc_final: 0.7443 (t70) REVERT: E 53 ARG cc_start: 0.8531 (tpp80) cc_final: 0.7981 (ttm170) REVERT: E 90 SER cc_start: 0.8203 (t) cc_final: 0.7690 (p) REVERT: E 101 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7027 (mp0) REVERT: E 201 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8281 (mm-40) REVERT: E 202 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7691 (mmtm) REVERT: F 44 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7587 (tm-30) REVERT: F 47 ARG cc_start: 0.7287 (mtp180) cc_final: 0.7015 (mtp-110) REVERT: F 67 GLU cc_start: 0.7576 (tp30) cc_final: 0.6917 (tp30) REVERT: F 70 ARG cc_start: 0.7575 (ttp80) cc_final: 0.6836 (ttp80) REVERT: F 101 VAL cc_start: 0.8579 (t) cc_final: 0.8290 (m) REVERT: F 134 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7449 (mm) REVERT: F 149 ASP cc_start: 0.7212 (m-30) cc_final: 0.6998 (m-30) REVERT: F 167 LEU cc_start: 0.8427 (pp) cc_final: 0.8213 (pp) REVERT: F 168 LEU cc_start: 0.8860 (tp) cc_final: 0.8513 (tp) REVERT: F 171 PHE cc_start: 0.8277 (t80) cc_final: 0.7787 (t80) REVERT: F 192 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7498 (mmmt) REVERT: F 202 LYS cc_start: 0.7562 (mttt) cc_final: 0.7152 (mttt) REVERT: F 211 PHE cc_start: 0.8349 (t80) cc_final: 0.8137 (t80) REVERT: F 223 GLU cc_start: 0.7901 (mp0) cc_final: 0.7219 (mp0) REVERT: F 225 LEU cc_start: 0.8332 (mt) cc_final: 0.7893 (mt) REVERT: F 226 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6908 (mm-30) REVERT: F 228 LEU cc_start: 0.8891 (mt) cc_final: 0.8460 (mt) REVERT: F 241 GLU cc_start: 0.6413 (tm-30) cc_final: 0.5678 (tm-30) REVERT: F 245 ILE cc_start: 0.8048 (mt) cc_final: 0.7478 (mt) REVERT: F 256 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7367 (ptpt) REVERT: F 259 SER cc_start: 0.8278 (m) cc_final: 0.7912 (t) REVERT: A 7 LEU cc_start: 0.8405 (tp) cc_final: 0.8161 (tt) REVERT: A 105 SER cc_start: 0.8061 (p) cc_final: 0.7849 (p) REVERT: A 165 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7738 (mmmt) REVERT: A 168 LEU cc_start: 0.8327 (mt) cc_final: 0.7911 (mt) REVERT: A 170 LYS cc_start: 0.8472 (mttt) cc_final: 0.8040 (mttt) REVERT: A 212 ARG cc_start: 0.7579 (mmm160) cc_final: 0.7127 (mmm160) REVERT: A 246 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: B 27 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 31 ILE cc_start: 0.8758 (mt) cc_final: 0.8386 (mp) REVERT: B 34 SER cc_start: 0.8424 (m) cc_final: 0.8189 (p) REVERT: B 101 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6706 (mp0) REVERT: B 131 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6845 (mp0) REVERT: B 133 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7684 (mp10) REVERT: B 202 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7742 (mmtm) REVERT: C 44 GLN cc_start: 0.8059 (tt0) cc_final: 0.7655 (tm-30) REVERT: C 48 GLN cc_start: 0.8179 (tt0) cc_final: 0.7675 (tt0) REVERT: C 69 LYS cc_start: 0.8084 (tptm) cc_final: 0.7035 (tptt) REVERT: C 73 LEU cc_start: 0.8197 (mm) cc_final: 0.7942 (mm) REVERT: C 134 LEU cc_start: 0.7720 (mm) cc_final: 0.7495 (mm) REVERT: C 158 TYR cc_start: 0.6447 (m-10) cc_final: 0.6133 (m-10) REVERT: C 171 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7694 (t80) REVERT: C 175 ASP cc_start: 0.7768 (p0) cc_final: 0.7283 (p0) REVERT: C 179 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7571 (mtm110) REVERT: C 202 LYS cc_start: 0.7951 (mttt) cc_final: 0.7708 (mttt) REVERT: C 203 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8145 (tm-30) REVERT: C 206 ASN cc_start: 0.7245 (t0) cc_final: 0.6889 (t0) REVERT: C 241 GLU cc_start: 0.6209 (tm-30) cc_final: 0.5757 (tm-30) REVERT: C 263 TYR cc_start: 0.6713 (p90) cc_final: 0.6350 (p90) REVERT: C 305 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7722 (mm) outliers start: 59 outliers final: 38 residues processed: 540 average time/residue: 0.1489 time to fit residues: 111.9241 Evaluate side-chains 554 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 511 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 D residue 181 ASP Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 130 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 88 THR Chi-restraints excluded: chain F residue 95 VAL 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 136 CYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 GLN 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 99 SER 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 95 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN A 30 ASN A 193 HIS B 146 HIS ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3843 r_free = 0.3843 target = 0.140837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110780 restraints weight = 25859.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114510 restraints weight = 11945.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116887 restraints weight = 7221.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118373 restraints weight = 5222.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119191 restraints weight = 4293.950| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15692 Z= 0.164 Angle : 0.605 9.163 21696 Z= 0.316 Chirality : 0.043 0.260 2412 Planarity : 0.004 0.050 2466 Dihedral : 19.159 88.255 2758 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.40 % Allowed : 18.41 % Favored : 77.20 % 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: 0.24 (0.21), residues: 1640 helix: 1.02 (0.19), residues: 766 sheet: 0.23 (0.33), residues: 220 loop : -0.84 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 177 TYR 0.023 0.002 TYR C 199 PHE 0.027 0.002 PHE C 150 TRP 0.019 0.001 TRP C 65 HIS 0.007 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (15676) covalent geometry : angle 0.60218 / 0.32 (21688) hydrogen bonds : bond 0.04345 / 3.02 ( 655) hydrogen bonds : angle 4.69393 / 3.34 ( 1881) metal coordination : bond 0.02321 / 1.32 ( 16) metal coordination : angle 2.85925 / 1.39 ( 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 595 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 531 time to evaluate : 0.520 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: 0.7355 (ptpp) cc_final: 0.6908 (ptpp) REVERT: D 165 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8032 (mmmt) REVERT: D 170 LYS cc_start: 0.8502 (mttt) cc_final: 0.8169 (mttt) REVERT: D 186 VAL cc_start: 0.8580 (t) cc_final: 0.8250 (p) REVERT: D 212 ARG cc_start: 0.7373 (mmm160) cc_final: 0.7044 (mmm160) REVERT: D 233 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8436 (mtmm) REVERT: D 246 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: D 273 LEU cc_start: 0.8555 (mt) cc_final: 0.8333 (mm) REVERT: E 30 ASN cc_start: 0.8015 (m-40) cc_final: 0.7689 (m-40) REVERT: E 31 ILE cc_start: 0.8677 (mp) cc_final: 0.8150 (tp) REVERT: E 34 SER cc_start: 0.8376 (m) cc_final: 0.8128 (p) REVERT: E 36 HIS cc_start: 0.7727 (t70) cc_final: 0.7413 (t70) REVERT: E 53 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8185 (ttm-80) REVERT: E 90 SER cc_start: 0.8175 (t) cc_final: 0.7650 (p) REVERT: E 101 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7014 (mp0) REVERT: E 178 LEU cc_start: 0.8718 (tp) cc_final: 0.8474 (tt) REVERT: E 201 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8273 (mm-40) REVERT: E 202 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7665 (mmtm) REVERT: E 237 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8188 (pt) REVERT: F 47 ARG cc_start: 0.7323 (mtp180) cc_final: 0.7077 (mtp-110) REVERT: F 67 GLU cc_start: 0.7617 (tp30) cc_final: 0.6998 (tp30) REVERT: F 69 LYS cc_start: 0.8243 (tttt) cc_final: 0.7745 (tptm) REVERT: F 70 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7190 (ttp80) REVERT: F 101 VAL cc_start: 0.8569 (t) cc_final: 0.8307 (m) REVERT: F 134 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7418 (mm) REVERT: F 149 ASP cc_start: 0.7340 (m-30) cc_final: 0.7134 (m-30) REVERT: F 168 LEU cc_start: 0.8857 (tp) cc_final: 0.8511 (tp) REVERT: F 171 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7814 (t80) REVERT: F 192 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7497 (mmmt) REVERT: F 202 LYS cc_start: 0.7640 (mttt) cc_final: 0.7217 (mttt) REVERT: F 211 PHE cc_start: 0.8339 (t80) cc_final: 0.8129 (t80) REVERT: F 223 GLU cc_start: 0.7932 (mp0) cc_final: 0.7107 (mp0) REVERT: F 225 LEU cc_start: 0.8327 (mt) cc_final: 0.7773 (mt) REVERT: F 226 GLU cc_start: 0.7647 (mm-30) cc_final: 0.6898 (mm-30) REVERT: F 228 LEU cc_start: 0.8897 (mt) cc_final: 0.8453 (mt) REVERT: F 241 GLU cc_start: 0.6481 (tm-30) cc_final: 0.5668 (tm-30) REVERT: F 245 ILE cc_start: 0.8044 (mt) cc_final: 0.7448 (mt) REVERT: F 256 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7457 (ptpt) REVERT: F 259 SER cc_start: 0.8302 (m) cc_final: 0.7919 (t) REVERT: A 7 LEU cc_start: 0.8426 (tp) cc_final: 0.8174 (tt) REVERT: A 105 SER cc_start: 0.8015 (p) cc_final: 0.7806 (p) REVERT: A 119 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7248 (tt) REVERT: A 139 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 165 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7783 (mmmt) REVERT: A 168 LEU cc_start: 0.8363 (mt) cc_final: 0.8039 (mt) REVERT: A 170 LYS cc_start: 0.8465 (mttt) cc_final: 0.7964 (mttt) REVERT: A 212 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7168 (mmm160) REVERT: B 27 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 31 ILE cc_start: 0.8738 (mt) cc_final: 0.8438 (mt) REVERT: B 34 SER cc_start: 0.8424 (m) cc_final: 0.8190 (p) REVERT: B 44 GLN cc_start: 0.8043 (mp10) cc_final: 0.7753 (mp10) REVERT: B 101 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6697 (mp0) REVERT: B 133 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: B 202 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7821 (mmtm) REVERT: C 44 GLN cc_start: 0.8027 (tt0) cc_final: 0.7559 (tm-30) REVERT: C 48 GLN cc_start: 0.8167 (tt0) cc_final: 0.7687 (tm-30) REVERT: C 69 LYS cc_start: 0.8087 (tptm) cc_final: 0.7161 (tptt) REVERT: C 95 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 128 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 134 LEU cc_start: 0.7810 (mm) cc_final: 0.7385 (mm) REVERT: C 165 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7338 (mm) REVERT: C 171 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 175 ASP cc_start: 0.7805 (p0) cc_final: 0.7139 (p0) REVERT: C 179 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7501 (mtm110) REVERT: C 202 LYS cc_start: 0.7992 (mttt) cc_final: 0.7716 (mttt) REVERT: C 206 ASN cc_start: 0.7306 (t0) cc_final: 0.6925 (t0) REVERT: C 241 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5726 (tm-30) REVERT: C 263 TYR cc_start: 0.6700 (p90) cc_final: 0.6305 (p90) REVERT: C 305 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7719 (mm) outliers start: 64 outliers final: 36 residues processed: 550 average time/residue: 0.1501 time to fit residues: 115.2422 Evaluate side-chains 572 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 525 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 134 HIS Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain E residue 75 LEU 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 E residue 237 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 95 VAL 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 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 A residue 139 LEU 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 82 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 118 HIS E 133 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 246 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109809 restraints weight = 25855.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113549 restraints weight = 12021.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115906 restraints weight = 7323.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117374 restraints weight = 5350.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118241 restraints weight = 4405.245| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15692 Z= 0.174 Angle : 0.611 8.136 21696 Z= 0.320 Chirality : 0.043 0.218 2412 Planarity : 0.004 0.046 2466 Dihedral : 19.260 89.817 2758 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.91 % Allowed : 20.26 % Favored : 75.82 % 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: 0.99 (0.19), residues: 770 sheet: 0.24 (0.33), residues: 220 loop : -0.80 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 177 TYR 0.021 0.002 TYR C 199 PHE 0.026 0.002 PHE C 150 TRP 0.014 0.001 TRP C 65 HIS 0.007 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (15676) covalent geometry : angle 0.60784 / 0.32 (21688) hydrogen bonds : bond 0.04305 / 2.99 ( 655) hydrogen bonds : angle 4.65669 / 3.30 ( 1881) metal coordination : bond 0.02594 / 1.43 ( 16) metal coordination : angle 3.18867 / 1.61 ( 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 593 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 536 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7367 (ptpp) cc_final: 0.6945 (ptpp) REVERT: D 142 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6533 (ptt-90) REVERT: D 165 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8009 (mmmt) REVERT: D 170 LYS cc_start: 0.8520 (mttt) cc_final: 0.7828 (mttt) REVERT: D 186 VAL cc_start: 0.8610 (t) cc_final: 0.8262 (p) REVERT: D 212 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7056 (mmm160) REVERT: D 233 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8437 (mtmm) REVERT: D 246 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: D 273 LEU cc_start: 0.8551 (mt) cc_final: 0.8338 (mm) REVERT: E 30 ASN cc_start: 0.8048 (m-40) cc_final: 0.7654 (m-40) REVERT: E 31 ILE cc_start: 0.8688 (mt) cc_final: 0.8196 (tp) REVERT: E 34 SER cc_start: 0.8372 (m) cc_final: 0.8130 (p) REVERT: E 36 HIS cc_start: 0.7687 (t70) cc_final: 0.7255 (t70) REVERT: E 40 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7864 (mtmm) REVERT: E 53 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8188 (ttm-80) REVERT: E 90 SER cc_start: 0.8165 (t) cc_final: 0.7663 (p) REVERT: E 101 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7024 (mp0) REVERT: E 178 LEU cc_start: 0.8731 (tp) cc_final: 0.8501 (tt) REVERT: E 201 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8244 (mm-40) REVERT: E 202 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7713 (mmtm) REVERT: E 268 ILE cc_start: 0.8595 (mm) cc_final: 0.8139 (tp) REVERT: F 44 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7494 (tm-30) REVERT: F 45 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8771 (ttmm) REVERT: F 47 ARG cc_start: 0.7296 (mtp180) cc_final: 0.7063 (mtp-110) REVERT: F 48 GLN cc_start: 0.8149 (tt0) cc_final: 0.7713 (tt0) REVERT: F 67 GLU cc_start: 0.7634 (tp30) cc_final: 0.7027 (tp30) REVERT: F 69 LYS cc_start: 0.8253 (tttt) cc_final: 0.7828 (tttp) REVERT: F 70 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7231 (ttp80) REVERT: F 101 VAL cc_start: 0.8554 (t) cc_final: 0.8296 (m) REVERT: F 134 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7411 (mm) REVERT: F 168 LEU cc_start: 0.8863 (tp) cc_final: 0.8544 (tp) REVERT: F 171 PHE cc_start: 0.8262 (t80) cc_final: 0.7823 (t80) REVERT: F 192 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7501 (mmmt) REVERT: F 202 LYS cc_start: 0.7699 (mttt) cc_final: 0.7266 (mttt) REVERT: F 203 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8051 (tm-30) REVERT: F 211 PHE cc_start: 0.8342 (t80) cc_final: 0.8139 (t80) REVERT: F 223 GLU cc_start: 0.7940 (mp0) cc_final: 0.7201 (mp0) REVERT: F 225 LEU cc_start: 0.8335 (mt) cc_final: 0.7755 (mt) REVERT: F 226 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6910 (mm-30) REVERT: F 228 LEU cc_start: 0.8898 (mt) cc_final: 0.8458 (mt) REVERT: F 241 GLU cc_start: 0.6514 (tm-30) cc_final: 0.5658 (tm-30) REVERT: F 245 ILE cc_start: 0.8026 (mt) cc_final: 0.7446 (mt) REVERT: F 259 SER cc_start: 0.8345 (m) cc_final: 0.7913 (t) REVERT: A 7 LEU cc_start: 0.8413 (tp) cc_final: 0.8157 (tt) REVERT: A 123 ASN cc_start: 0.8230 (t0) cc_final: 0.7905 (t0) REVERT: A 133 GLN cc_start: 0.7249 (tp40) cc_final: 0.6956 (mp10) REVERT: A 139 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 165 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7793 (mmmt) REVERT: A 168 LEU cc_start: 0.8351 (mt) cc_final: 0.8059 (mt) REVERT: A 212 ARG cc_start: 0.7610 (mmm160) cc_final: 0.7172 (mmm160) REVERT: A 246 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: B 27 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 31 ILE cc_start: 0.8751 (mt) cc_final: 0.8449 (mt) REVERT: B 34 SER cc_start: 0.8454 (m) cc_final: 0.8196 (p) REVERT: B 72 LYS cc_start: 0.8410 (mptt) cc_final: 0.8208 (mptt) REVERT: B 101 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6571 (mp0) REVERT: B 133 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: B 201 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8340 (mm110) REVERT: B 202 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7902 (mmtm) REVERT: B 268 ILE cc_start: 0.8572 (mm) cc_final: 0.8094 (tp) REVERT: C 44 GLN cc_start: 0.8009 (tt0) cc_final: 0.7619 (tm-30) REVERT: C 48 GLN cc_start: 0.8196 (tt0) cc_final: 0.7678 (tm-30) REVERT: C 69 LYS cc_start: 0.8027 (tptm) cc_final: 0.7662 (tppt) REVERT: C 95 VAL cc_start: 0.8435 (m) cc_final: 0.8176 (p) REVERT: C 165 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7324 (mm) REVERT: C 171 PHE cc_start: 0.7917 (m-80) cc_final: 0.7590 (t80) REVERT: C 175 ASP cc_start: 0.7792 (p0) cc_final: 0.7200 (p0) REVERT: C 179 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7561 (mtm110) REVERT: C 202 LYS cc_start: 0.8019 (mttt) cc_final: 0.7743 (mttt) REVERT: C 203 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8073 (mm-40) REVERT: C 210 ARG cc_start: 0.7516 (mtt90) cc_final: 0.7135 (mtm180) REVERT: C 241 GLU cc_start: 0.6365 (tm-30) cc_final: 0.5785 (tm-30) REVERT: C 263 TYR cc_start: 0.6752 (p90) cc_final: 0.6035 (p90) REVERT: C 266 GLN cc_start: 0.7664 (mp10) cc_final: 0.7279 (mp10) REVERT: C 305 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7703 (mm) outliers start: 57 outliers final: 36 residues processed: 555 average time/residue: 0.1455 time to fit residues: 112.4761 Evaluate side-chains 578 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 534 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 141 ILE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 130 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 98 MET 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 139 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 GLN 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 99 SER 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 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 Chi-restraints excluded: chain C residue 305 LEU 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 250 GLN E 79 HIS E 118 HIS E 133 GLN F 102 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS A 30 ASN A 209 HIS A 246 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110340 restraints weight = 25731.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114054 restraints weight = 11880.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116409 restraints weight = 7203.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117761 restraints weight = 5247.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118759 restraints weight = 4354.471| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15692 Z= 0.171 Angle : 0.627 7.633 21696 Z= 0.328 Chirality : 0.043 0.279 2412 Planarity : 0.004 0.040 2466 Dihedral : 19.273 89.139 2758 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.85 % Allowed : 21.29 % Favored : 74.86 % 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: 0.28 (0.21), residues: 1640 helix: 1.04 (0.19), residues: 766 sheet: 0.17 (0.33), residues: 220 loop : -0.77 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 115 TYR 0.015 0.002 TYR C 199 PHE 0.028 0.002 PHE C 163 TRP 0.015 0.001 TRP B 205 HIS 0.005 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (15676) covalent geometry : angle 0.62523 / 0.33 (21688) hydrogen bonds : bond 0.04234 / 2.94 ( 655) hydrogen bonds : angle 4.67811 / 3.32 ( 1881) metal coordination : bond 0.02453 / 1.37 ( 16) metal coordination : angle 2.77962 / 1.39 ( 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 592 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 536 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 LYS cc_start: 0.7410 (ptpp) cc_final: 0.6968 (ptpp) REVERT: D 142 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6486 (ptt-90) REVERT: D 165 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8034 (mmmt) REVERT: D 170 LYS cc_start: 0.8527 (mttt) cc_final: 0.8221 (mttt) REVERT: D 186 VAL cc_start: 0.8590 (t) cc_final: 0.8259 (p) REVERT: D 212 ARG cc_start: 0.7371 (mmm160) cc_final: 0.7109 (mmm160) REVERT: D 233 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8426 (mtmm) REVERT: D 273 LEU cc_start: 0.8557 (mt) cc_final: 0.8337 (mm) REVERT: E 30 ASN cc_start: 0.8035 (m-40) cc_final: 0.7666 (m-40) REVERT: E 31 ILE cc_start: 0.8688 (mt) cc_final: 0.8194 (tp) REVERT: E 34 SER cc_start: 0.8372 (m) cc_final: 0.8131 (p) REVERT: E 36 HIS cc_start: 0.7700 (t70) cc_final: 0.7154 (t70) REVERT: E 40 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7830 (mtmm) REVERT: E 53 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8181 (ttm-80) REVERT: E 90 SER cc_start: 0.8167 (t) cc_final: 0.7642 (p) REVERT: E 101 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7025 (mp0) REVERT: E 178 LEU cc_start: 0.8680 (tp) cc_final: 0.8437 (tt) REVERT: E 201 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8250 (mm-40) REVERT: E 202 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7694 (mmtm) REVERT: E 268 ILE cc_start: 0.8580 (mm) cc_final: 0.8148 (tp) REVERT: F 44 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 47 ARG cc_start: 0.7327 (mtp180) cc_final: 0.7108 (mtp-110) REVERT: F 48 GLN cc_start: 0.8169 (tt0) cc_final: 0.7714 (tt0) REVERT: F 67 GLU cc_start: 0.7674 (tp30) cc_final: 0.6498 (tp30) REVERT: F 69 LYS cc_start: 0.8337 (tttt) cc_final: 0.7959 (tttp) REVERT: F 70 ARG cc_start: 0.7531 (ttp80) cc_final: 0.6526 (ttp80) REVERT: F 101 VAL cc_start: 0.8541 (t) cc_final: 0.8269 (m) REVERT: F 134 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7423 (mm) REVERT: F 168 LEU cc_start: 0.8884 (tp) cc_final: 0.8568 (tp) REVERT: F 171 PHE cc_start: 0.8268 (t80) cc_final: 0.7887 (t80) REVERT: F 202 LYS cc_start: 0.7829 (mttt) cc_final: 0.7399 (mttt) REVERT: F 203 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8064 (tm-30) REVERT: F 211 PHE cc_start: 0.8341 (t80) cc_final: 0.8137 (t80) REVERT: F 223 GLU cc_start: 0.8035 (mp0) cc_final: 0.7413 (mp0) REVERT: F 225 LEU cc_start: 0.8402 (mt) cc_final: 0.7815 (mt) REVERT: F 226 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7006 (mm-30) REVERT: F 228 LEU cc_start: 0.8909 (mt) cc_final: 0.8453 (mt) REVERT: F 241 GLU cc_start: 0.6561 (tm-30) cc_final: 0.5673 (tm-30) REVERT: F 245 ILE cc_start: 0.8045 (mt) cc_final: 0.7476 (mt) REVERT: F 259 SER cc_start: 0.8312 (m) cc_final: 0.7849 (t) REVERT: A 7 LEU cc_start: 0.8379 (tp) cc_final: 0.8145 (tt) REVERT: A 19 THR cc_start: 0.8235 (m) cc_final: 0.7826 (p) REVERT: A 136 CYS cc_start: 0.7039 (p) cc_final: 0.6778 (p) REVERT: A 139 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 165 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7865 (mmmt) REVERT: A 168 LEU cc_start: 0.8365 (mt) cc_final: 0.8096 (mt) REVERT: A 212 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7100 (mmm160) REVERT: B 31 ILE cc_start: 0.8724 (mt) cc_final: 0.8407 (mt) REVERT: B 34 SER cc_start: 0.8463 (m) cc_final: 0.8206 (p) REVERT: B 72 LYS cc_start: 0.8464 (mptt) cc_final: 0.8255 (mptt) REVERT: B 96 ARG cc_start: 0.7493 (pmt170) cc_final: 0.6638 (pmt170) REVERT: B 101 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6676 (mp0) REVERT: B 133 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: B 201 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8377 (mm110) REVERT: B 202 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7895 (mmtm) REVERT: B 268 ILE cc_start: 0.8557 (mm) cc_final: 0.8034 (tp) REVERT: C 44 GLN cc_start: 0.8044 (tt0) cc_final: 0.7648 (tm-30) REVERT: C 48 GLN cc_start: 0.8219 (tt0) cc_final: 0.7676 (tm-30) REVERT: C 69 LYS cc_start: 0.8007 (tptm) cc_final: 0.7587 (tppt) REVERT: C 134 LEU cc_start: 0.7831 (mm) cc_final: 0.7501 (mm) REVERT: C 165 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7291 (mm) REVERT: C 171 PHE cc_start: 0.7940 (m-80) cc_final: 0.7607 (t80) REVERT: C 175 ASP cc_start: 0.7787 (p0) cc_final: 0.7161 (p0) REVERT: C 179 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7538 (mtm110) REVERT: C 199 TYR cc_start: 0.6858 (t80) cc_final: 0.6462 (t80) REVERT: C 202 LYS cc_start: 0.8067 (mttt) cc_final: 0.7803 (mttt) REVERT: C 203 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8143 (tm-30) REVERT: C 241 GLU cc_start: 0.6417 (tm-30) cc_final: 0.5751 (tm-30) REVERT: C 263 TYR cc_start: 0.6934 (p90) cc_final: 0.6525 (p90) REVERT: C 305 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (mm) outliers start: 56 outliers final: 41 residues processed: 557 average time/residue: 0.1527 time to fit residues: 118.0247 Evaluate side-chains 580 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 533 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 141 ILE Chi-restraints excluded: chain D residue 142 ARG 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 75 LEU Chi-restraints excluded: chain E residue 110 ILE 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 39 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 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 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 139 LEU Chi-restraints excluded: chain A residue 141 ILE 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 99 SER 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 135 GLN Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 ASP 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 Chi-restraints excluded: chain C residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 163 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 199 HIS D 209 HIS D 246 GLN D 250 GLN E 118 HIS E 133 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN C 166 GLN C 217 HIS C 218 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110338 restraints weight = 25797.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114162 restraints weight = 11907.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116579 restraints weight = 7224.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118110 restraints weight = 5253.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119029 restraints weight = 4312.091| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15692 Z= 0.157 Angle : 0.635 9.913 21696 Z= 0.331 Chirality : 0.043 0.252 2412 Planarity : 0.004 0.045 2466 Dihedral : 19.238 88.685 2758 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.98 % Allowed : 22.12 % Favored : 73.90 % 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: 0.31 (0.21), residues: 1640 helix: 1.06 (0.19), residues: 766 sheet: 0.15 (0.33), residues: 220 loop : -0.72 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 115 TYR 0.016 0.001 TYR B 169 PHE 0.027 0.002 PHE C 150 TRP 0.015 0.001 TRP B 205 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (15676) covalent geometry : angle 0.63346 / 0.33 (21688) hydrogen bonds : bond 0.04099 / 2.85 ( 655) hydrogen bonds : angle 4.63611 / 3.28 ( 1881) metal coordination : bond 0.02031 / 1.15 ( 16) metal coordination : angle 2.17447 / 1.07 ( 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 595 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 537 time to evaluate : 0.539 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: D 133 GLN cc_start: 0.7411 (tp40) cc_final: 0.7098 (mp10) REVERT: D 142 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6442 (ptt-90) REVERT: D 165 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7998 (mmmt) REVERT: D 170 LYS cc_start: 0.8495 (mttt) cc_final: 0.8141 (mttt) REVERT: D 186 VAL cc_start: 0.8588 (t) cc_final: 0.8252 (p) REVERT: D 204 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8331 (mtt90) REVERT: D 212 ARG cc_start: 0.7363 (mmm160) cc_final: 0.7094 (mmm160) REVERT: D 233 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8425 (mtmm) REVERT: D 273 LEU cc_start: 0.8556 (mt) cc_final: 0.8335 (mm) REVERT: E 27 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7366 (mt-10) REVERT: E 31 ILE cc_start: 0.8696 (mt) cc_final: 0.8211 (tp) REVERT: E 34 SER cc_start: 0.8330 (m) cc_final: 0.8059 (p) REVERT: E 36 HIS cc_start: 0.7677 (t70) cc_final: 0.7382 (t70) REVERT: E 47 MET cc_start: 0.8053 (mmm) cc_final: 0.7685 (tpp) REVERT: E 53 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8178 (ttm-80) REVERT: E 90 SER cc_start: 0.8157 (t) cc_final: 0.7637 (p) REVERT: E 101 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7016 (mp0) REVERT: E 178 LEU cc_start: 0.8687 (tp) cc_final: 0.8445 (tt) REVERT: E 201 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8230 (mm-40) REVERT: E 202 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7697 (mmtm) REVERT: E 268 ILE cc_start: 0.8586 (mm) cc_final: 0.8150 (tp) REVERT: F 44 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7535 (tm-30) REVERT: F 47 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7095 (mtp-110) REVERT: F 48 GLN cc_start: 0.8106 (tt0) cc_final: 0.7707 (tt0) REVERT: F 67 GLU cc_start: 0.7658 (tp30) cc_final: 0.6506 (tp30) REVERT: F 69 LYS cc_start: 0.8352 (tttt) cc_final: 0.8022 (tttp) REVERT: F 70 ARG cc_start: 0.7512 (ttp80) cc_final: 0.6504 (ttp80) REVERT: F 101 VAL cc_start: 0.8553 (t) cc_final: 0.8252 (m) REVERT: F 134 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7405 (mm) REVERT: F 171 PHE cc_start: 0.8217 (t80) cc_final: 0.7828 (t80) REVERT: F 202 LYS cc_start: 0.7864 (mttt) cc_final: 0.7435 (mttt) REVERT: F 203 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8038 (tm-30) REVERT: F 211 PHE cc_start: 0.8272 (t80) cc_final: 0.8070 (t80) REVERT: F 223 GLU cc_start: 0.8021 (mp0) cc_final: 0.7293 (mp0) REVERT: F 225 LEU cc_start: 0.8414 (mt) cc_final: 0.7825 (mt) REVERT: F 226 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7003 (mm-30) REVERT: F 228 LEU cc_start: 0.8897 (mt) cc_final: 0.8543 (mt) REVERT: F 241 GLU cc_start: 0.6556 (tm-30) cc_final: 0.5675 (tm-30) REVERT: F 245 ILE cc_start: 0.8045 (mt) cc_final: 0.7477 (mt) REVERT: F 259 SER cc_start: 0.8295 (m) cc_final: 0.7831 (t) REVERT: F 283 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7098 (tm-30) REVERT: F 287 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6174 (ptp) REVERT: A 7 LEU cc_start: 0.8331 (tp) cc_final: 0.8096 (tt) REVERT: A 86 SER cc_start: 0.8233 (m) cc_final: 0.7933 (p) REVERT: A 136 CYS cc_start: 0.7035 (p) cc_final: 0.6764 (p) REVERT: A 139 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 165 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7815 (mmmt) REVERT: A 168 LEU cc_start: 0.8383 (mt) cc_final: 0.8168 (mt) REVERT: A 170 LYS cc_start: 0.8469 (mttt) cc_final: 0.7947 (mttt) REVERT: A 212 ARG cc_start: 0.7577 (mmm160) cc_final: 0.7059 (mmm160) REVERT: B 31 ILE cc_start: 0.8735 (mt) cc_final: 0.8405 (mt) REVERT: B 34 SER cc_start: 0.8450 (m) cc_final: 0.8172 (p) REVERT: B 44 GLN cc_start: 0.8085 (mp10) cc_final: 0.7846 (mp10) REVERT: B 72 LYS cc_start: 0.8495 (mptt) cc_final: 0.8241 (mptt) REVERT: B 96 ARG cc_start: 0.7497 (pmt170) cc_final: 0.6932 (pmt170) REVERT: B 101 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6743 (mp0) REVERT: B 133 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: B 201 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8368 (mm110) REVERT: B 202 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7890 (mmtm) REVERT: B 268 ILE cc_start: 0.8570 (mm) cc_final: 0.8078 (tp) REVERT: C 69 LYS cc_start: 0.8004 (tptm) cc_final: 0.7502 (tptt) REVERT: C 79 TYR cc_start: 0.6912 (t80) cc_final: 0.6324 (t80) REVERT: C 134 LEU cc_start: 0.7865 (mm) cc_final: 0.7469 (mm) REVERT: C 165 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7205 (mm) REVERT: C 166 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: C 171 PHE cc_start: 0.7905 (m-80) cc_final: 0.7597 (t80) REVERT: C 175 ASP cc_start: 0.7731 (p0) cc_final: 0.7049 (p0) REVERT: C 179 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7525 (mtm110) REVERT: C 199 TYR cc_start: 0.7042 (t80) cc_final: 0.6713 (t80) REVERT: C 202 LYS cc_start: 0.8074 (mttt) cc_final: 0.7758 (mttt) REVERT: C 210 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7419 (mtm180) REVERT: C 241 GLU cc_start: 0.6311 (tm-30) cc_final: 0.5639 (tm-30) REVERT: C 263 TYR cc_start: 0.6908 (p90) cc_final: 0.6106 (p90) REVERT: C 266 GLN cc_start: 0.7671 (mp10) cc_final: 0.7301 (mp10) REVERT: C 292 TYR cc_start: 0.7446 (m-80) cc_final: 0.7159 (m-80) REVERT: C 305 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7698 (mm) outliers start: 58 outliers final: 40 residues processed: 554 average time/residue: 0.1529 time to fit residues: 117.1024 Evaluate side-chains 581 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 533 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU 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 39 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 ILE 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 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 133 GLN Chi-restraints excluded: chain A residue 139 LEU 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 135 GLN Chi-restraints excluded: chain C residue 138 TYR 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 Chi-restraints excluded: chain C residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 131 optimal weight: 0.0980 chunk 163 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 HIS D 199 HIS D 209 HIS D 246 GLN D 250 GLN E 118 HIS E 133 GLN F 206 ASN A 133 GLN A 246 GLN B 68 HIS C 166 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112216 restraints weight = 25755.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116022 restraints weight = 11739.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118421 restraints weight = 7056.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119904 restraints weight = 5123.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120790 restraints weight = 4220.407| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15692 Z= 0.142 Angle : 0.636 10.871 21696 Z= 0.331 Chirality : 0.043 0.261 2412 Planarity : 0.004 0.045 2466 Dihedral : 19.188 88.445 2758 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.50 % Allowed : 23.28 % Favored : 73.21 % 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: 1.11 (0.19), residues: 766 sheet: 0.15 (0.32), residues: 220 loop : -0.66 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 177 TYR 0.016 0.001 TYR B 169 PHE 0.035 0.002 PHE C 163 TRP 0.013 0.001 TRP B 205 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15676) covalent geometry : angle 0.63500 / 0.33 (21688) hydrogen bonds : bond 0.03943 / 2.75 ( 655) hydrogen bonds : angle 4.61013 / 3.27 ( 1881) metal coordination : bond 0.01713 / 0.98 ( 16) metal coordination : angle 1.59941 / 0.77 ( 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 590 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 539 time to evaluate : 0.510 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: 0.7331 (ptpp) cc_final: 0.6905 (ptpp) REVERT: D 133 GLN cc_start: 0.7343 (tp40) cc_final: 0.7060 (mp10) REVERT: D 142 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6323 (ptt-90) REVERT: D 165 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7947 (mmmt) REVERT: D 170 LYS cc_start: 0.8607 (mttt) cc_final: 0.7904 (mttt) REVERT: D 186 VAL cc_start: 0.8592 (t) cc_final: 0.8252 (p) REVERT: D 204 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8339 (mtt90) REVERT: D 212 ARG cc_start: 0.7339 (mmm160) cc_final: 0.7072 (mmm160) REVERT: D 233 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8435 (mtmm) REVERT: D 273 LEU cc_start: 0.8565 (mt) cc_final: 0.8345 (mm) REVERT: E 27 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 31 ILE cc_start: 0.8715 (mt) cc_final: 0.8241 (tp) REVERT: E 34 SER cc_start: 0.8312 (m) cc_final: 0.8055 (p) REVERT: E 36 HIS cc_start: 0.7641 (t70) cc_final: 0.7353 (t70) REVERT: E 47 MET cc_start: 0.8016 (mmm) cc_final: 0.7680 (tpp) REVERT: E 53 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8172 (ttm-80) REVERT: E 66 ILE cc_start: 0.8525 (mt) cc_final: 0.8250 (tp) REVERT: E 90 SER cc_start: 0.8145 (t) cc_final: 0.7642 (p) REVERT: E 101 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6982 (mp0) REVERT: E 170 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8500 (mtmt) REVERT: E 178 LEU cc_start: 0.8678 (tp) cc_final: 0.8468 (tt) REVERT: E 201 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8226 (mm-40) REVERT: E 202 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7718 (mmtm) REVERT: F 44 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7544 (tm-30) REVERT: F 47 ARG cc_start: 0.7286 (mtp180) cc_final: 0.7082 (mtp-110) REVERT: F 48 GLN cc_start: 0.8097 (tt0) cc_final: 0.7687 (tt0) REVERT: F 67 GLU cc_start: 0.7644 (tp30) cc_final: 0.6562 (tp30) REVERT: F 69 LYS cc_start: 0.8355 (tttt) cc_final: 0.8012 (tttp) REVERT: F 70 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6512 (ttp80) REVERT: F 101 VAL cc_start: 0.8536 (t) cc_final: 0.8260 (m) REVERT: F 134 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7389 (mm) REVERT: F 171 PHE cc_start: 0.8180 (t80) cc_final: 0.7862 (t80) REVERT: F 202 LYS cc_start: 0.7850 (mttt) cc_final: 0.7425 (mttt) REVERT: F 223 GLU cc_start: 0.7972 (mp0) cc_final: 0.7354 (mp0) REVERT: F 225 LEU cc_start: 0.8397 (mt) cc_final: 0.7793 (mt) REVERT: F 226 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6967 (mm-30) REVERT: F 228 LEU cc_start: 0.8880 (mt) cc_final: 0.8616 (mm) REVERT: F 241 GLU cc_start: 0.6536 (tm-30) cc_final: 0.5622 (tm-30) REVERT: F 245 ILE cc_start: 0.7975 (mt) cc_final: 0.7389 (mt) REVERT: F 259 SER cc_start: 0.8296 (m) cc_final: 0.7932 (t) REVERT: F 283 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7019 (tm-30) REVERT: F 287 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6126 (ptp) REVERT: A 7 LEU cc_start: 0.8340 (tp) cc_final: 0.8092 (tt) REVERT: A 86 SER cc_start: 0.8209 (m) cc_final: 0.7906 (p) REVERT: A 132 PHE cc_start: 0.8328 (t80) cc_final: 0.7960 (t80) REVERT: A 136 CYS cc_start: 0.6962 (p) cc_final: 0.6703 (p) REVERT: A 139 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 165 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7769 (mmmt) REVERT: A 170 LYS cc_start: 0.8495 (mttt) cc_final: 0.7976 (mttt) REVERT: A 212 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7057 (mmm160) REVERT: B 31 ILE cc_start: 0.8752 (mt) cc_final: 0.8420 (mt) REVERT: B 34 SER cc_start: 0.8432 (m) cc_final: 0.8197 (p) REVERT: B 44 GLN cc_start: 0.8009 (mp10) cc_final: 0.7796 (mp10) REVERT: B 72 LYS cc_start: 0.8466 (mptt) cc_final: 0.8213 (mptt) REVERT: B 96 ARG cc_start: 0.7462 (pmt170) cc_final: 0.6618 (pmt170) REVERT: B 101 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6748 (mp0) REVERT: B 133 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: B 178 LEU cc_start: 0.8680 (tt) cc_final: 0.8434 (tp) REVERT: B 182 ASN cc_start: 0.8321 (m-40) cc_final: 0.8052 (m-40) REVERT: B 201 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8360 (mm110) REVERT: B 202 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7898 (mmtm) REVERT: B 268 ILE cc_start: 0.8571 (mm) cc_final: 0.8105 (tp) REVERT: C 69 LYS cc_start: 0.8002 (tptm) cc_final: 0.7525 (tppt) REVERT: C 79 TYR cc_start: 0.6927 (t80) cc_final: 0.6317 (t80) REVERT: C 163 PHE cc_start: 0.7161 (t80) cc_final: 0.6958 (t80) REVERT: C 165 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7255 (mm) REVERT: C 166 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6944 (mt0) REVERT: C 171 PHE cc_start: 0.7827 (m-80) cc_final: 0.7545 (t80) REVERT: C 175 ASP cc_start: 0.7643 (p0) cc_final: 0.7053 (p0) REVERT: C 179 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7404 (mtm110) REVERT: C 202 LYS cc_start: 0.8052 (mttt) cc_final: 0.7783 (mttt) REVERT: C 241 GLU cc_start: 0.6326 (tm-30) cc_final: 0.5594 (tm-30) REVERT: C 263 TYR cc_start: 0.6820 (p90) cc_final: 0.6057 (p90) REVERT: C 266 GLN cc_start: 0.7691 (mp10) cc_final: 0.7329 (mp10) REVERT: C 292 TYR cc_start: 0.7393 (m-80) cc_final: 0.7088 (m-80) REVERT: C 301 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6246 (mp0) REVERT: C 305 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7693 (mm) outliers start: 51 outliers final: 38 residues processed: 558 average time/residue: 0.1543 time to fit residues: 119.5330 Evaluate side-chains 578 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 532 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU 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 134 LEU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 146 GLU 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 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 139 LEU Chi-restraints excluded: chain A residue 181 ASP 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 138 TYR Chi-restraints excluded: chain C residue 143 ARG 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 Chi-restraints excluded: chain C residue 305 LEU 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: 1.9990 chunk 28 optimal weight: 0.4980 chunk 111 optimal weight: 0.4980 chunk 126 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 148 optimal weight: 0.0040 chunk 99 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 HIS D 209 HIS D 250 GLN E 118 HIS E 133 GLN F 206 ASN B 68 HIS C 166 GLN ** C 187 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 = 0.3860 r_free = 0.3860 target = 0.142304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112789 restraints weight = 25825.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116601 restraints weight = 11728.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118980 restraints weight = 7051.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120448 restraints weight = 5134.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121336 restraints weight = 4234.029| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15692 Z= 0.133 Angle : 0.642 9.522 21696 Z= 0.333 Chirality : 0.043 0.284 2412 Planarity : 0.004 0.078 2466 Dihedral : 19.127 88.168 2758 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.02 % Allowed : 23.90 % Favored : 73.08 % 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: 0.44 (0.21), residues: 1640 helix: 1.17 (0.19), residues: 764 sheet: 0.16 (0.32), residues: 220 loop : -0.64 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 177 TYR 0.015 0.001 TYR B 169 PHE 0.033 0.002 PHE C 163 TRP 0.014 0.001 TRP F 131 HIS 0.004 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15676) covalent geometry : angle 0.64160 / 0.33 (21688) hydrogen bonds : bond 0.03798 / 2.66 ( 655) hydrogen bonds : angle 4.55739 / 3.23 ( 1881) metal coordination : bond 0.01350 / 0.77 ( 16) metal coordination : angle 1.00963 / 0.47 ( 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 580 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 536 time to evaluate : 0.530 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 133 GLN cc_start: 0.7339 (tp40) cc_final: 0.7050 (mp10) REVERT: D 142 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6323 (ptt-90) REVERT: D 165 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7952 (mmmt) REVERT: D 170 LYS cc_start: 0.8621 (mttt) cc_final: 0.7943 (mttt) REVERT: D 186 VAL cc_start: 0.8577 (t) cc_final: 0.8241 (p) REVERT: D 204 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.8230 (mtt90) REVERT: D 212 ARG cc_start: 0.7329 (mmm160) cc_final: 0.7066 (mmm160) REVERT: D 233 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8433 (mtmm) REVERT: D 273 LEU cc_start: 0.8562 (mt) cc_final: 0.8339 (mm) REVERT: E 27 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7282 (mt-10) REVERT: E 31 ILE cc_start: 0.8721 (mt) cc_final: 0.8353 (mp) REVERT: E 34 SER cc_start: 0.8312 (m) cc_final: 0.8083 (p) REVERT: E 36 HIS cc_start: 0.7626 (t70) cc_final: 0.7333 (t70) REVERT: E 47 MET cc_start: 0.8006 (mmm) cc_final: 0.7688 (tpp) REVERT: E 53 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8174 (ttm-80) REVERT: E 101 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6963 (mp0) REVERT: E 170 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8489 (mtmt) REVERT: E 178 LEU cc_start: 0.8668 (tp) cc_final: 0.8462 (tt) REVERT: E 201 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8200 (mm110) REVERT: E 202 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7693 (mmtm) REVERT: E 268 ILE cc_start: 0.8673 (mm) cc_final: 0.8349 (tp) REVERT: F 44 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7567 (tm-30) REVERT: F 48 GLN cc_start: 0.8059 (tt0) cc_final: 0.7630 (tt0) REVERT: F 67 GLU cc_start: 0.7655 (tp30) cc_final: 0.6524 (tp30) REVERT: F 69 LYS cc_start: 0.8345 (tttt) cc_final: 0.7958 (tttp) REVERT: F 70 ARG cc_start: 0.7470 (ttp80) cc_final: 0.6585 (ttp80) REVERT: F 101 VAL cc_start: 0.8474 (t) cc_final: 0.8218 (m) REVERT: F 134 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7403 (mm) REVERT: F 201 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6922 (mmm-85) REVERT: F 202 LYS cc_start: 0.7911 (mttt) cc_final: 0.7492 (mttt) REVERT: F 225 LEU cc_start: 0.8393 (mt) cc_final: 0.7782 (mt) REVERT: F 226 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6963 (mm-30) REVERT: F 228 LEU cc_start: 0.8885 (mt) cc_final: 0.8615 (mm) REVERT: F 241 GLU cc_start: 0.6498 (tm-30) cc_final: 0.5575 (tm-30) REVERT: F 245 ILE cc_start: 0.7957 (mt) cc_final: 0.7363 (mt) REVERT: F 259 SER cc_start: 0.8283 (m) cc_final: 0.7906 (t) REVERT: F 283 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6925 (tm-30) REVERT: F 287 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6120 (ptp) REVERT: A 7 LEU cc_start: 0.8340 (tp) cc_final: 0.8084 (tt) REVERT: A 86 SER cc_start: 0.8185 (m) cc_final: 0.7884 (p) REVERT: A 136 CYS cc_start: 0.6957 (p) cc_final: 0.6678 (p) REVERT: A 139 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 165 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7784 (mmmt) REVERT: A 212 ARG cc_start: 0.7545 (mmm160) cc_final: 0.7022 (mmm160) REVERT: B 31 ILE cc_start: 0.8747 (mt) cc_final: 0.8412 (mt) REVERT: B 34 SER cc_start: 0.8412 (m) cc_final: 0.8179 (p) REVERT: B 72 LYS cc_start: 0.8473 (mptt) cc_final: 0.8219 (mptt) REVERT: B 96 ARG cc_start: 0.7448 (pmt170) cc_final: 0.6912 (pmt170) REVERT: B 101 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6737 (mp0) REVERT: B 133 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: B 178 LEU cc_start: 0.8564 (tt) cc_final: 0.8300 (tp) REVERT: B 182 ASN cc_start: 0.8298 (m-40) cc_final: 0.7966 (m-40) REVERT: B 268 ILE cc_start: 0.8579 (mm) cc_final: 0.8109 (tp) REVERT: C 69 LYS cc_start: 0.7988 (tptm) cc_final: 0.7525 (tptt) REVERT: C 79 TYR cc_start: 0.6922 (t80) cc_final: 0.6382 (t80) REVERT: C 163 PHE cc_start: 0.7210 (t80) cc_final: 0.6981 (t80) REVERT: C 165 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7254 (mm) REVERT: C 166 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6782 (mt0) REVERT: C 171 PHE cc_start: 0.7820 (m-80) cc_final: 0.7557 (t80) REVERT: C 202 LYS cc_start: 0.8050 (mttt) cc_final: 0.7778 (mttt) REVERT: C 226 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 241 GLU cc_start: 0.6326 (tm-30) cc_final: 0.5588 (tm-30) REVERT: C 263 TYR cc_start: 0.6814 (p90) cc_final: 0.6047 (p90) REVERT: C 266 GLN cc_start: 0.7693 (mp10) cc_final: 0.7313 (mp10) REVERT: C 292 TYR cc_start: 0.7415 (m-80) cc_final: 0.7006 (m-80) REVERT: C 301 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6357 (mp0) outliers start: 44 outliers final: 30 residues processed: 556 average time/residue: 0.1529 time to fit residues: 117.5867 Evaluate side-chains 565 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 528 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 20 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 110 ILE 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 134 LEU Chi-restraints excluded: chain F residue 135 GLN 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 139 LEU Chi-restraints excluded: chain A residue 181 ASP 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 210 SER Chi-restraints excluded: chain C residue 138 TYR 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: 1.9990 chunk 149 optimal weight: 0.0070 chunk 108 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 209 HIS D 250 GLN E 118 HIS E 133 GLN F 206 ASN B 68 HIS ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112384 restraints weight = 25662.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116125 restraints weight = 11648.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118501 restraints weight = 7036.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119948 restraints weight = 5149.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120826 restraints weight = 4258.113| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15692 Z= 0.144 Angle : 0.651 8.990 21696 Z= 0.337 Chirality : 0.043 0.272 2412 Planarity : 0.004 0.071 2466 Dihedral : 19.104 87.903 2758 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.68 % Allowed : 24.73 % Favored : 72.60 % 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: 0.44 (0.21), residues: 1640 helix: 1.17 (0.19), residues: 768 sheet: 0.12 (0.32), residues: 220 loop : -0.63 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 39 TYR 0.014 0.001 TYR E 169 PHE 0.038 0.002 PHE F 163 TRP 0.015 0.001 TRP B 205 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (15676) covalent geometry : angle 0.65027 / 0.34 (21688) hydrogen bonds : bond 0.03804 / 2.66 ( 655) hydrogen bonds : angle 4.58374 / 3.25 ( 1881) metal coordination : bond 0.01745 / 0.98 ( 16) metal coordination : angle 1.20821 / 0.59 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.14 seconds wall clock time: 58 minutes 47.11 seconds (3527.11 seconds total)