Starting phenix.real_space_refine on Sat Aug 23 07:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k26_36829/08_2025/8k26_36829.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6722 2.51 5 N 1815 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2292 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 2314 Chain: "E" Number of atoms: 2343 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 2375 Chain: "d" Number of atoms: 2296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 289, 2286 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2326 Chain: "e" Number of atoms: 2326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2318 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 295, 2318 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2358 Chain: "A" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 649 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "a" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 643 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.52, per 1000 atoms: 0.43 Number of scatterers: 10549 At special positions: 0 Unit cell: (81.2278, 87.927, 157.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1954 8.00 N 1815 7.00 C 6722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 855.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 54.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.853A pdb=" N ASN D 67 " --> pdb=" O MET D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 4.417A pdb=" N MET D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 132 removed outlier: 4.282A pdb=" N ARG D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.582A pdb=" N ALA D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.628A pdb=" N ALA D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 4.094A pdb=" N ASP D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.019A pdb=" N THR D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.819A pdb=" N LEU D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 280 removed outlier: 3.513A pdb=" N PHE D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.801A pdb=" N LEU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 110 through 132 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 161 through 184 Processing helix chain 'E' and resid 196 through 221 Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.847A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 280 through 294 removed outlier: 4.112A pdb=" N TYR E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 10 removed outlier: 3.571A pdb=" N GLN d 9 " --> pdb=" O LEU d 6 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS d 10 " --> pdb=" O THR d 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 6 through 10' Processing helix chain 'd' and resid 57 through 67 removed outlier: 3.542A pdb=" N MET d 61 " --> pdb=" O THR d 57 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 109 removed outlier: 4.411A pdb=" N MET d 101 " --> pdb=" O PRO d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 132 removed outlier: 4.038A pdb=" N ARG d 125 " --> pdb=" O ILE d 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL d 126 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP d 127 " --> pdb=" O LYS d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 159 removed outlier: 3.574A pdb=" N ALA d 159 " --> pdb=" O GLY d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 180 removed outlier: 3.803A pdb=" N TYR d 180 " --> pdb=" O LEU d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 183 No H-bonds generated for 'chain 'd' and resid 181 through 183' Processing helix chain 'd' and resid 196 through 220 removed outlier: 3.515A pdb=" N LYS d 200 " --> pdb=" O ASP d 196 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN d 206 " --> pdb=" O LEU d 202 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR d 207 " --> pdb=" O THR d 203 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR d 208 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA d 209 " --> pdb=" O GLY d 205 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA d 219 " --> pdb=" O SER d 215 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU d 220 " --> pdb=" O SER d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 261 removed outlier: 4.223A pdb=" N ASP d 241 " --> pdb=" O GLY d 237 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE d 245 " --> pdb=" O ASP d 241 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE d 246 " --> pdb=" O VAL d 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR d 248 " --> pdb=" O ASP d 244 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER d 249 " --> pdb=" O ILE d 245 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE d 250 " --> pdb=" O ILE d 246 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU d 252 " --> pdb=" O THR d 248 " (cutoff:3.500A) Proline residue: d 253 - end of helix Processing helix chain 'd' and resid 264 through 279 removed outlier: 3.601A pdb=" N PHE d 268 " --> pdb=" O SER d 264 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN d 279 " --> pdb=" O TYR d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 280 through 294 removed outlier: 3.623A pdb=" N ARG d 291 " --> pdb=" O ASN d 287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU d 292 " --> pdb=" O ASN d 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 65 Processing helix chain 'e' and resid 98 through 110 removed outlier: 3.656A pdb=" N GLN e 102 " --> pdb=" O THR e 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP e 110 " --> pdb=" O ARG e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 132 Processing helix chain 'e' and resid 142 through 159 Processing helix chain 'e' and resid 161 through 184 Processing helix chain 'e' and resid 196 through 221 Processing helix chain 'e' and resid 236 through 248 removed outlier: 3.558A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE e 245 " --> pdb=" O ASP e 241 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE e 246 " --> pdb=" O VAL e 242 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 262 Processing helix chain 'e' and resid 264 through 279 Processing helix chain 'e' and resid 280 through 295 removed outlier: 4.149A pdb=" N MET e 294 " --> pdb=" O LYS e 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU e 295 " --> pdb=" O ARG e 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.534A pdb=" N GLY A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 23 removed outlier: 3.683A pdb=" N ALA a 23 " --> pdb=" O ARG a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 removed outlier: 4.041A pdb=" N GLY a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16 removed outlier: 5.828A pdb=" N ASN D 12 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D 47 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR D 14 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 71 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN E 12 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY E 49 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR E 14 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AA3, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.638A pdb=" N ILE D 56 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 56 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL E 23 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 15 through 16 removed outlier: 3.790A pdb=" N VAL d 71 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN e 12 " --> pdb=" O PHE e 47 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY e 49 " --> pdb=" O ASN e 12 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR e 14 " --> pdb=" O GLY e 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 27 through 31 removed outlier: 3.814A pdb=" N ILE d 56 " --> pdb=" O ILE e 56 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE e 56 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL e 23 " --> pdb=" O THR e 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.695A pdb=" N GLU A 26 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 34 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 68 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 62 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 26 through 27 removed outlier: 3.662A pdb=" N GLU a 26 " --> pdb=" O GLU a 34 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU a 34 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE a 68 " --> pdb=" O CYS a 60 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR a 62 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL a 66 " --> pdb=" O TYR a 62 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2209 1.33 - 1.45: 2537 1.45 - 1.57: 5923 1.57 - 1.70: 4 1.70 - 1.82: 92 Bond restraints: 10765 Sorted by residual: bond pdb=" CA TRP D 218 " pdb=" C TRP D 218 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.32e-02 5.74e+03 1.78e+01 bond pdb=" CA PHE D 226 " pdb=" C PHE D 226 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.00e-02 1.00e+04 8.90e+00 bond pdb=" CB ASN e 279 " pdb=" CG ASN e 279 " ideal model delta sigma weight residual 1.516 1.589 -0.073 2.50e-02 1.60e+03 8.47e+00 bond pdb=" CA MET D 294 " pdb=" CB MET D 294 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.36e-02 5.41e+03 7.57e+00 bond pdb=" C PHE E 226 " pdb=" N PRO E 227 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 10760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 14215 3.85 - 7.70: 278 7.70 - 11.55: 46 11.55 - 15.41: 4 15.41 - 19.26: 2 Bond angle restraints: 14545 Sorted by residual: angle pdb=" N ILE D 222 " pdb=" CA ILE D 222 " pdb=" C ILE D 222 " ideal model delta sigma weight residual 108.36 127.62 -19.26 1.43e+00 4.89e-01 1.81e+02 angle pdb=" N GLY D 221 " pdb=" CA GLY D 221 " pdb=" C GLY D 221 " ideal model delta sigma weight residual 113.18 128.19 -15.01 2.37e+00 1.78e-01 4.01e+01 angle pdb=" CB LYS e 154 " pdb=" CG LYS e 154 " pdb=" CD LYS e 154 " ideal model delta sigma weight residual 111.30 125.47 -14.17 2.30e+00 1.89e-01 3.80e+01 angle pdb=" N GLY d 237 " pdb=" CA GLY d 237 " pdb=" C GLY d 237 " ideal model delta sigma weight residual 111.21 117.26 -6.05 1.04e+00 9.25e-01 3.39e+01 angle pdb=" CA ASN e 279 " pdb=" CB ASN e 279 " pdb=" CG ASN e 279 " ideal model delta sigma weight residual 112.60 118.28 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 14540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5377 17.73 - 35.45: 820 35.45 - 53.18: 181 53.18 - 70.91: 24 70.91 - 88.64: 16 Dihedral angle restraints: 6418 sinusoidal: 2504 harmonic: 3914 Sorted by residual: dihedral pdb=" CA TYR d 184 " pdb=" C TYR d 184 " pdb=" N GLU d 185 " pdb=" CA GLU d 185 " ideal model delta harmonic sigma weight residual 180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU d 6 " pdb=" C LEU d 6 " pdb=" N THR d 7 " pdb=" CA THR d 7 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLN D 261 " pdb=" C GLN D 261 " pdb=" N GLY D 262 " pdb=" CA GLY D 262 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 6415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1450 0.104 - 0.208: 145 0.208 - 0.312: 18 0.312 - 0.416: 5 0.416 - 0.520: 1 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CA GLN d 4 " pdb=" N GLN d 4 " pdb=" C GLN d 4 " pdb=" CB GLN d 4 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CA ILE D 222 " pdb=" N ILE D 222 " pdb=" C ILE D 222 " pdb=" CB ILE D 222 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE e 250 " pdb=" CA ILE e 250 " pdb=" CG1 ILE e 250 " pdb=" CG2 ILE e 250 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1616 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL a 81 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO a 82 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO a 82 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO a 82 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 108 " -0.027 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP E 108 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 108 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 108 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 108 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 108 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 104 " -0.023 2.00e-02 2.50e+03 1.86e-02 8.64e+00 pdb=" CG TRP E 104 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 104 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 104 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 104 " -0.007 2.00e-02 2.50e+03 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1367 2.76 - 3.29: 10389 3.29 - 3.83: 19229 3.83 - 4.36: 21722 4.36 - 4.90: 35948 Nonbonded interactions: 88655 Sorted by model distance: nonbonded pdb=" OD1 ASP d 135 " pdb=" OH TYR d 275 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN D 9 " pdb=" OE1 GLN a 40 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLN e 27 " pdb=" OG1 THR e 39 " model vdw 2.261 3.040 nonbonded pdb=" O TYR e 79 " pdb=" OG SER e 215 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN D 27 " pdb=" OG SER a 22 " model vdw 2.282 3.040 ... (remaining 88650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 84)) selection = chain 'a' } ncs_group { reference = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 105 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 113 or (resid 11 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 115 through \ 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) or re \ sid 125 through 128 or (resid 129 and (name N or name CA or name C or name O or \ name CB )) or resid 130 through 149 or resid 151 or (resid 152 through 153 and ( \ name N or name CA or name C or name O or name CB )) or resid 154 through 161 or \ (resid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 165 or (resid 166 and (name N or name CA or name C or name O or name CB \ )) or resid 167 through 192 or (resid 193 and (name N or name CA or name C or n \ ame O or name CB )) or resid 194 through 227 or (resid 228 and (name N or name C \ A or name C or name O or name CB )) or resid 229 through 276 or (resid 277 throu \ gh 278 and (name N or name CA or name C or name O or name CB )) or resid 279 thr \ ough 281 or (resid 282 through 283 and (name N or name CA or name C or name O or \ name CB )) or resid 284 through 285 or (resid 286 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 through 295)) selection = (chain 'E' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 75 or resid 83 through 10 \ 5 or resid 107 through 113 or (resid 114 and (name N or name CA or name C or nam \ e O or name CB )) or resid 115 through 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB )) or resid 130 through 149 or resid 151 or (resi \ d 152 through 153 and (name N or name CA or name C or name O or name CB )) or re \ sid 154 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 217 or (resid 218 through 219 an \ d (name N or name CA or name C or name O or name CB )) or resid 220 through 225 \ or (resid 226 and (name N or name CA or name C or name O or name CB )) or resid \ 227 or (resid 228 and (name N or name CA or name C or name O or name CB )) or re \ sid 229 through 276 or (resid 277 through 278 and (name N or name CA or name C o \ r name O or name CB )) or resid 279 through 281 or (resid 282 through 283 and (n \ ame N or name CA or name C or name O or name CB )) or resid 284 or (resid 285 th \ rough 286 and (name N or name CA or name C or name O or name CB )) or resid 288 \ through 291 or (resid 292 and (name N or name CA or name C or name O or name CB \ )) or resid 293 or (resid 294 and (name N or name CA or name C or name O or name \ CB )) or resid 295)) selection = (chain 'd' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 100 or (resid 101 and (na \ me N or name CA or name C or name O or name CB )) or resid 102 through 105 or re \ sid 107 through 113 or (resid 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 149 or resid 151 \ or (resid 152 through 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 through 161 or (resid 162 and (name N or name CA or name C or n \ ame O or name CB )) or resid 163 through 165 or (resid 166 and (name N or name C \ A or name C or name O or name CB )) or resid 167 through 192 or (resid 193 and ( \ name N or name CA or name C or name O or name CB )) or resid 194 through 217 or \ (resid 218 through 219 and (name N or name CA or name C or name O or name CB )) \ or resid 220 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 284 or (resid 285 through 286 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 291 or (res \ id 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ )) selection = (chain 'e' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 75 or resid 83 through 10 \ 0 or (resid 101 and (name N or name CA or name C or name O or name CB )) or resi \ d 102 through 105 or (resid 107 and (name N or name CA or name C or name O or na \ me CB )) or resid 108 through 149 or resid 151 through 161 or (resid 162 and (na \ me N or name CA or name C or name O or name CB )) or resid 163 through 217 or (r \ esid 218 through 219 and (name N or name CA or name C or name O or name CB )) or \ resid 220 through 225 or (resid 226 and (name N or name CA or name C or name O \ or name CB )) or resid 227 through 276 or (resid 277 through 278 and (name N or \ name CA or name C or name O or name CB )) or resid 279 through 281 or (resid 282 \ through 283 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 84 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 288 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.780 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 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 : 0.006 0.096 10765 Z= 0.307 Angle : 1.309 19.257 14545 Z= 0.712 Chirality : 0.070 0.520 1619 Planarity : 0.008 0.104 1845 Dihedral : 17.744 88.635 3908 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 0.71 % Allowed : 29.62 % Favored : 69.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -3.00 (0.20), residues: 1325 helix: -1.89 (0.16), residues: 664 sheet: -0.58 (0.52), residues: 106 loop : -2.27 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 11 TYR 0.050 0.003 TYR e 180 PHE 0.040 0.004 PHE e 226 TRP 0.065 0.006 TRP E 108 HIS 0.021 0.003 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00636 (10765) covalent geometry : angle 1.30930 (14545) hydrogen bonds : bond 0.13869 ( 567) hydrogen bonds : angle 7.22819 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 MET cc_start: 0.2874 (mtt) cc_final: 0.2278 (ttp) REVERT: D 245 ILE cc_start: 0.6426 (mm) cc_final: 0.5228 (mm) REVERT: E 61 MET cc_start: 0.3411 (mtm) cc_final: 0.3035 (mtp) REVERT: d 73 TRP cc_start: 0.4312 (m100) cc_final: 0.3274 (m100) REVERT: d 294 MET cc_start: -0.1245 (mtt) cc_final: -0.1748 (mtt) REVERT: e 101 MET cc_start: 0.4668 (mmm) cc_final: 0.2690 (tpt) REVERT: e 279 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7787 (t0) REVERT: A 16 LYS cc_start: 0.8871 (tppt) cc_final: 0.8466 (tppt) REVERT: A 20 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6870 (mp0) outliers start: 8 outliers final: 2 residues processed: 155 average time/residue: 0.1151 time to fit residues: 25.1628 Evaluate side-chains 143 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 279 ASN Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 67 ASN E 206 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN a 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.200068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.153571 restraints weight = 58236.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.165278 restraints weight = 20668.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.171894 restraints weight = 10444.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.171273 restraints weight = 8042.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.172380 restraints weight = 7152.050| |-----------------------------------------------------------------------------| r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10765 Z= 0.165 Angle : 0.727 7.302 14545 Z= 0.386 Chirality : 0.045 0.167 1619 Planarity : 0.005 0.108 1845 Dihedral : 6.348 40.046 1463 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.32 % Favored : 95.45 % Rotamer: Outliers : 3.09 % Allowed : 27.85 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.78 (0.22), residues: 1325 helix: -0.52 (0.19), residues: 675 sheet: -0.43 (0.47), residues: 126 loop : -2.20 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 214 TYR 0.019 0.002 TYR E 284 PHE 0.027 0.002 PHE d 72 TRP 0.028 0.003 TRP e 73 HIS 0.008 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00375 (10765) covalent geometry : angle 0.72667 (14545) hydrogen bonds : bond 0.04585 ( 567) hydrogen bonds : angle 5.11673 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6778 (p90) cc_final: 0.5497 (p90) REVERT: D 141 GLU cc_start: 0.0441 (OUTLIER) cc_final: 0.0101 (mt-10) REVERT: D 204 LEU cc_start: 0.6384 (tp) cc_final: 0.5810 (tt) REVERT: E 13 MET cc_start: 0.2286 (mmt) cc_final: 0.2069 (mmt) REVERT: E 61 MET cc_start: 0.3790 (mtm) cc_final: 0.3119 (mpp) REVERT: E 81 MET cc_start: 0.8475 (tmm) cc_final: 0.8221 (tmm) REVERT: d 141 GLU cc_start: 0.3259 (OUTLIER) cc_final: 0.2793 (pp20) REVERT: d 294 MET cc_start: -0.1581 (OUTLIER) cc_final: -0.1802 (mtp) REVERT: a 4 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.4725 (ttp80) outliers start: 35 outliers final: 14 residues processed: 168 average time/residue: 0.1045 time to fit residues: 25.2831 Evaluate side-chains 146 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 141 GLU Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN A 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.199781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.151006 restraints weight = 64170.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.162051 restraints weight = 20743.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.168984 restraints weight = 10767.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.170112 restraints weight = 7083.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.171038 restraints weight = 6546.097| |-----------------------------------------------------------------------------| r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10765 Z= 0.137 Angle : 0.674 10.219 14545 Z= 0.356 Chirality : 0.045 0.156 1619 Planarity : 0.005 0.107 1845 Dihedral : 5.720 24.292 1457 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.38 % Favored : 94.39 % Rotamer: Outliers : 2.48 % Allowed : 27.32 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.27 (0.22), residues: 1325 helix: 0.08 (0.20), residues: 675 sheet: -0.19 (0.47), residues: 126 loop : -2.25 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 11 TYR 0.017 0.001 TYR E 284 PHE 0.020 0.002 PHE d 72 TRP 0.034 0.002 TRP E 108 HIS 0.009 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00307 (10765) covalent geometry : angle 0.67414 (14545) hydrogen bonds : bond 0.04015 ( 567) hydrogen bonds : angle 4.85216 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6986 (p90) cc_final: 0.5721 (p90) REVERT: D 89 HIS cc_start: 0.7231 (m90) cc_final: 0.6942 (m170) REVERT: D 204 LEU cc_start: 0.6388 (tp) cc_final: 0.5821 (tt) REVERT: D 270 ARG cc_start: 0.6449 (tpm170) cc_final: 0.5066 (tpm170) REVERT: E 132 HIS cc_start: 0.4672 (m-70) cc_final: 0.4276 (t-90) REVERT: d 214 ARG cc_start: 0.3067 (OUTLIER) cc_final: 0.2558 (mmm160) REVERT: d 294 MET cc_start: -0.1759 (OUTLIER) cc_final: -0.2005 (mtp) REVERT: e 81 MET cc_start: 0.6236 (tmm) cc_final: 0.5774 (ttt) REVERT: e 101 MET cc_start: 0.5086 (mmm) cc_final: 0.3092 (tpt) REVERT: A 19 ARG cc_start: 0.7425 (mmm160) cc_final: 0.7102 (mmm160) REVERT: a 4 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.4966 (ttp80) outliers start: 28 outliers final: 13 residues processed: 158 average time/residue: 0.1093 time to fit residues: 24.4769 Evaluate side-chains 137 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 129 optimal weight: 0.0170 chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 GLN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.200709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.153098 restraints weight = 75572.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.163780 restraints weight = 23389.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.168751 restraints weight = 12581.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.171346 restraints weight = 7835.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.172359 restraints weight = 7323.762| |-----------------------------------------------------------------------------| r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4861 r_free = 0.4861 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4861 r_free = 0.4861 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10765 Z= 0.129 Angle : 0.656 8.689 14545 Z= 0.343 Chirality : 0.045 0.245 1619 Planarity : 0.004 0.106 1845 Dihedral : 5.511 23.464 1457 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.77 % Favored : 95.00 % Rotamer: Outliers : 2.92 % Allowed : 26.17 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.97 (0.23), residues: 1325 helix: 0.42 (0.20), residues: 667 sheet: -0.14 (0.47), residues: 125 loop : -2.18 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 214 TYR 0.016 0.001 TYR E 207 PHE 0.020 0.002 PHE d 72 TRP 0.017 0.002 TRP d 108 HIS 0.007 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00289 (10765) covalent geometry : angle 0.65582 (14545) hydrogen bonds : bond 0.03831 ( 567) hydrogen bonds : angle 4.66034 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.494 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 47 PHE cc_start: 0.6836 (p90) cc_final: 0.5718 (p90) REVERT: D 204 LEU cc_start: 0.6223 (tp) cc_final: 0.5699 (tt) REVERT: E 132 HIS cc_start: 0.4897 (m-70) cc_final: 0.4492 (t-90) REVERT: E 294 MET cc_start: 0.6439 (ptp) cc_final: 0.6219 (ptp) REVERT: d 124 MET cc_start: 0.1369 (ptp) cc_final: 0.0952 (ptt) REVERT: d 214 ARG cc_start: 0.2888 (OUTLIER) cc_final: 0.2518 (mmm160) REVERT: d 294 MET cc_start: -0.1811 (OUTLIER) cc_final: -0.2085 (mtp) REVERT: A 24 TYR cc_start: 0.7279 (m-80) cc_final: 0.6853 (m-80) REVERT: A 75 MET cc_start: 0.6795 (tmm) cc_final: 0.6373 (tmm) REVERT: a 4 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5134 (ttp80) REVERT: a 65 LYS cc_start: 0.2605 (OUTLIER) cc_final: 0.2052 (pttt) outliers start: 33 outliers final: 16 residues processed: 161 average time/residue: 0.1120 time to fit residues: 25.4432 Evaluate side-chains 145 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain d residue 13 MET Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN a 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.192368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.143123 restraints weight = 71471.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.154454 restraints weight = 23738.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.158995 restraints weight = 11571.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.159608 restraints weight = 8353.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.161093 restraints weight = 8025.107| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4725 r_free = 0.4725 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4725 r_free = 0.4725 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 10765 Z= 0.227 Angle : 0.742 8.542 14545 Z= 0.391 Chirality : 0.047 0.248 1619 Planarity : 0.005 0.103 1845 Dihedral : 5.771 25.086 1457 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.14 % Favored : 93.64 % Rotamer: Outliers : 3.63 % Allowed : 25.91 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.21 (0.22), residues: 1325 helix: 0.19 (0.20), residues: 681 sheet: -0.42 (0.46), residues: 123 loop : -2.23 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 11 TYR 0.017 0.002 TYR E 207 PHE 0.026 0.002 PHE e 72 TRP 0.028 0.003 TRP E 108 HIS 0.008 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00520 (10765) covalent geometry : angle 0.74249 (14545) hydrogen bonds : bond 0.04410 ( 567) hydrogen bonds : angle 5.02120 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6567 (tp) cc_final: 0.6155 (tt) REVERT: E 132 HIS cc_start: 0.4876 (m-70) cc_final: 0.4405 (t-90) REVERT: E 294 MET cc_start: 0.6509 (ptp) cc_final: 0.6245 (ptp) REVERT: d 1 MET cc_start: 0.4871 (pmm) cc_final: 0.3617 (ttt) REVERT: d 22 LEU cc_start: 0.6929 (pp) cc_final: 0.6175 (tp) REVERT: d 215 SER cc_start: 0.2735 (OUTLIER) cc_final: 0.2145 (t) REVERT: d 294 MET cc_start: -0.1409 (OUTLIER) cc_final: -0.1755 (mtp) REVERT: e 81 MET cc_start: 0.6522 (tmm) cc_final: 0.5925 (ttt) REVERT: e 101 MET cc_start: 0.5379 (mmm) cc_final: 0.3046 (tpt) REVERT: A 20 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 30 ASN cc_start: 0.6911 (t0) cc_final: 0.6347 (t0) REVERT: a 4 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.4830 (ttp-170) REVERT: a 65 LYS cc_start: 0.2723 (OUTLIER) cc_final: 0.2219 (pttt) outliers start: 41 outliers final: 24 residues processed: 161 average time/residue: 0.1013 time to fit residues: 23.2738 Evaluate side-chains 146 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 230 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.194762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.146448 restraints weight = 63176.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.156042 restraints weight = 21480.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.162180 restraints weight = 12314.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.164840 restraints weight = 7739.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.165473 restraints weight = 7283.553| |-----------------------------------------------------------------------------| r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4792 r_free = 0.4792 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4792 r_free = 0.4792 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10765 Z= 0.153 Angle : 0.699 11.848 14545 Z= 0.359 Chirality : 0.045 0.254 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.591 27.243 1457 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 3.27 % Allowed : 26.44 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.98 (0.22), residues: 1325 helix: 0.49 (0.20), residues: 662 sheet: -0.29 (0.47), residues: 125 loop : -2.23 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 270 TYR 0.015 0.002 TYR E 284 PHE 0.022 0.002 PHE d 72 TRP 0.029 0.003 TRP E 108 HIS 0.018 0.001 HIS e 257 Details of bonding type rmsd covalent geometry : bond 0.00351 (10765) covalent geometry : angle 0.69884 (14545) hydrogen bonds : bond 0.03937 ( 567) hydrogen bonds : angle 4.83646 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.367 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 204 LEU cc_start: 0.6294 (tp) cc_final: 0.5845 (tt) REVERT: E 132 HIS cc_start: 0.4981 (m-70) cc_final: 0.4519 (t-90) REVERT: E 294 MET cc_start: 0.6470 (ptp) cc_final: 0.6127 (ptp) REVERT: d 1 MET cc_start: 0.4813 (pmm) cc_final: 0.3602 (ttt) REVERT: d 13 MET cc_start: 0.7481 (mtm) cc_final: 0.6909 (mtm) REVERT: d 124 MET cc_start: 0.2246 (ptp) cc_final: 0.1699 (ptt) REVERT: d 214 ARG cc_start: 0.3252 (OUTLIER) cc_final: 0.2692 (mmm160) REVERT: e 101 MET cc_start: 0.5538 (mmm) cc_final: 0.3340 (tpt) REVERT: A 30 ASN cc_start: 0.6907 (t0) cc_final: 0.6358 (t0) REVERT: a 4 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.4752 (ttp80) REVERT: a 65 LYS cc_start: 0.2988 (OUTLIER) cc_final: 0.2448 (pttt) outliers start: 37 outliers final: 19 residues processed: 152 average time/residue: 0.1099 time to fit residues: 23.6929 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 81 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 134 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 192 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN A 31 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.195115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.146844 restraints weight = 71587.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.157378 restraints weight = 22801.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.162221 restraints weight = 12132.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.163949 restraints weight = 8254.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.165209 restraints weight = 7531.528| |-----------------------------------------------------------------------------| r_work (final): 0.4774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4775 r_free = 0.4775 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4775 r_free = 0.4775 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10765 Z= 0.151 Angle : 0.689 9.770 14545 Z= 0.354 Chirality : 0.045 0.275 1619 Planarity : 0.004 0.103 1845 Dihedral : 5.470 25.565 1457 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.21 % Favored : 93.56 % Rotamer: Outliers : 3.01 % Allowed : 26.26 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.89 (0.23), residues: 1325 helix: 0.55 (0.20), residues: 664 sheet: -0.27 (0.48), residues: 126 loop : -2.16 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 96 TYR 0.021 0.002 TYR A 24 PHE 0.020 0.002 PHE d 72 TRP 0.030 0.002 TRP E 108 HIS 0.017 0.002 HIS e 257 Details of bonding type rmsd covalent geometry : bond 0.00349 (10765) covalent geometry : angle 0.68870 (14545) hydrogen bonds : bond 0.03857 ( 567) hydrogen bonds : angle 4.82587 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6269 (tp) cc_final: 0.5855 (tt) REVERT: E 132 HIS cc_start: 0.5200 (m-70) cc_final: 0.4699 (t-90) REVERT: E 294 MET cc_start: 0.6623 (ptp) cc_final: 0.6368 (ptp) REVERT: d 1 MET cc_start: 0.4876 (pmm) cc_final: 0.3846 (ttt) REVERT: d 22 LEU cc_start: 0.6823 (pp) cc_final: 0.6059 (tp) REVERT: d 124 MET cc_start: 0.2290 (ptp) cc_final: 0.1755 (ptt) REVERT: d 136 PHE cc_start: 0.2263 (OUTLIER) cc_final: 0.1797 (p90) REVERT: d 214 ARG cc_start: 0.3076 (OUTLIER) cc_final: 0.2824 (tpt90) REVERT: d 215 SER cc_start: 0.2519 (OUTLIER) cc_final: 0.1731 (t) REVERT: e 101 MET cc_start: 0.5687 (mmm) cc_final: 0.3525 (tpt) REVERT: A 30 ASN cc_start: 0.6980 (t0) cc_final: 0.6390 (t0) REVERT: a 4 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.4613 (ttp80) REVERT: a 65 LYS cc_start: 0.2751 (OUTLIER) cc_final: 0.2266 (pttt) outliers start: 34 outliers final: 24 residues processed: 155 average time/residue: 0.1055 time to fit residues: 23.4885 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 81 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 HIS A 31 ASN A 51 ASN ** a 61 ASN ** 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 = 0.5156 r_free = 0.5156 target = 0.198009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.159651 restraints weight = 68259.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.167774 restraints weight = 30118.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.170905 restraints weight = 16590.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.171273 restraints weight = 12216.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.172068 restraints weight = 12550.743| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4721 r_free = 0.4721 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4721 r_free = 0.4721 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10765 Z= 0.172 Angle : 0.715 11.017 14545 Z= 0.369 Chirality : 0.046 0.292 1619 Planarity : 0.004 0.102 1845 Dihedral : 5.527 25.325 1457 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.21 % Favored : 93.56 % Rotamer: Outliers : 3.45 % Allowed : 25.82 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.89 (0.23), residues: 1325 helix: 0.55 (0.20), residues: 664 sheet: -0.33 (0.48), residues: 126 loop : -2.16 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 96 TYR 0.019 0.002 TYR A 24 PHE 0.022 0.002 PHE d 72 TRP 0.029 0.003 TRP E 108 HIS 0.015 0.001 HIS e 257 Details of bonding type rmsd covalent geometry : bond 0.00398 (10765) covalent geometry : angle 0.71477 (14545) hydrogen bonds : bond 0.03962 ( 567) hydrogen bonds : angle 4.92667 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6701 (tp) cc_final: 0.6234 (tt) REVERT: E 132 HIS cc_start: 0.4638 (m-70) cc_final: 0.4359 (t-90) REVERT: d 1 MET cc_start: 0.4892 (pmm) cc_final: 0.3918 (ttt) REVERT: d 124 MET cc_start: 0.2549 (ptp) cc_final: 0.1971 (ptt) REVERT: d 136 PHE cc_start: 0.3153 (OUTLIER) cc_final: 0.2256 (p90) REVERT: d 214 ARG cc_start: 0.3473 (OUTLIER) cc_final: 0.2883 (mmm160) REVERT: d 215 SER cc_start: 0.2900 (OUTLIER) cc_final: 0.2274 (t) REVERT: d 252 LEU cc_start: -0.3299 (OUTLIER) cc_final: -0.3516 (tp) REVERT: d 263 MET cc_start: 0.6632 (pmm) cc_final: 0.5715 (pmm) REVERT: e 101 MET cc_start: 0.5515 (mmm) cc_final: 0.3630 (tpt) REVERT: e 178 LYS cc_start: 0.8845 (pttp) cc_final: 0.8511 (pttm) REVERT: a 4 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.4329 (ttp80) REVERT: a 65 LYS cc_start: 0.3001 (OUTLIER) cc_final: 0.2341 (pttt) outliers start: 39 outliers final: 27 residues processed: 152 average time/residue: 0.1016 time to fit residues: 22.2585 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.195389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.159069 restraints weight = 74769.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.166167 restraints weight = 35941.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.169814 restraints weight = 17297.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.170133 restraints weight = 13179.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.171604 restraints weight = 12192.055| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.4730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10765 Z= 0.211 Angle : 0.755 10.185 14545 Z= 0.394 Chirality : 0.048 0.300 1619 Planarity : 0.005 0.103 1845 Dihedral : 5.744 25.443 1457 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.59 % Favored : 93.18 % Rotamer: Outliers : 3.09 % Allowed : 26.08 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.06 (0.23), residues: 1325 helix: 0.36 (0.19), residues: 674 sheet: -0.55 (0.48), residues: 125 loop : -2.17 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 19 TYR 0.020 0.002 TYR A 24 PHE 0.024 0.002 PHE e 72 TRP 0.028 0.003 TRP E 108 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00482 (10765) covalent geometry : angle 0.75488 (14545) hydrogen bonds : bond 0.04268 ( 567) hydrogen bonds : angle 5.12845 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7233 (p90) cc_final: 0.5672 (p90) REVERT: D 185 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6757 (tp30) REVERT: D 204 LEU cc_start: 0.6680 (tp) cc_final: 0.6338 (tt) REVERT: d 1 MET cc_start: 0.4784 (pmm) cc_final: 0.3774 (ttt) REVERT: d 124 MET cc_start: 0.2885 (ptp) cc_final: 0.2207 (ptt) REVERT: d 136 PHE cc_start: 0.3352 (OUTLIER) cc_final: 0.2070 (p90) REVERT: d 215 SER cc_start: 0.3201 (OUTLIER) cc_final: 0.2534 (t) REVERT: d 252 LEU cc_start: -0.2842 (OUTLIER) cc_final: -0.3047 (tp) REVERT: d 263 MET cc_start: 0.6500 (pmm) cc_final: 0.5645 (pmm) REVERT: e 101 MET cc_start: 0.5504 (mmm) cc_final: 0.3851 (tpt) REVERT: e 178 LYS cc_start: 0.8729 (pttp) cc_final: 0.8487 (pttm) REVERT: a 4 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.4251 (ttp80) REVERT: a 65 LYS cc_start: 0.2958 (OUTLIER) cc_final: 0.2427 (pttt) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.1035 time to fit residues: 22.5281 Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 252 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.0020 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.189384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.141893 restraints weight = 56045.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.153646 restraints weight = 21070.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.155291 restraints weight = 10965.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.156509 restraints weight = 8637.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.158361 restraints weight = 8029.313| |-----------------------------------------------------------------------------| r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.4656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10765 Z= 0.204 Angle : 0.763 10.486 14545 Z= 0.400 Chirality : 0.048 0.305 1619 Planarity : 0.005 0.104 1845 Dihedral : 5.764 25.648 1457 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.52 % Favored : 93.26 % Rotamer: Outliers : 2.92 % Allowed : 26.61 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.08 (0.23), residues: 1325 helix: 0.34 (0.19), residues: 671 sheet: -0.61 (0.48), residues: 125 loop : -2.14 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 270 TYR 0.023 0.002 TYR A 24 PHE 0.024 0.002 PHE d 72 TRP 0.028 0.003 TRP E 108 HIS 0.009 0.002 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00468 (10765) covalent geometry : angle 0.76323 (14545) hydrogen bonds : bond 0.04234 ( 567) hydrogen bonds : angle 5.13719 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.410 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 47 PHE cc_start: 0.7219 (p90) cc_final: 0.5672 (p90) REVERT: D 185 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7121 (tp30) REVERT: D 204 LEU cc_start: 0.6127 (tp) cc_final: 0.5825 (tt) REVERT: d 1 MET cc_start: 0.4482 (pmm) cc_final: 0.3538 (ttt) REVERT: d 124 MET cc_start: 0.3170 (ptp) cc_final: 0.2366 (ptt) REVERT: d 136 PHE cc_start: 0.3494 (OUTLIER) cc_final: 0.1974 (p90) REVERT: d 215 SER cc_start: 0.2888 (OUTLIER) cc_final: 0.1991 (t) REVERT: d 252 LEU cc_start: -0.2725 (OUTLIER) cc_final: -0.2930 (tp) REVERT: d 263 MET cc_start: 0.6551 (pmm) cc_final: 0.5671 (pmm) REVERT: e 101 MET cc_start: 0.5821 (mmm) cc_final: 0.4285 (tpt) REVERT: a 4 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.4059 (ttp80) REVERT: a 65 LYS cc_start: 0.3025 (OUTLIER) cc_final: 0.2498 (pttt) outliers start: 33 outliers final: 28 residues processed: 144 average time/residue: 0.1059 time to fit residues: 22.0793 Evaluate side-chains 151 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 252 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 chunk 104 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 230 HIS ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.195975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.156806 restraints weight = 75288.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.165199 restraints weight = 33241.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.169219 restraints weight = 17239.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.168649 restraints weight = 13131.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.170604 restraints weight = 12619.050| |-----------------------------------------------------------------------------| r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4695 r_free = 0.4695 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4695 r_free = 0.4695 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.4695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10765 Z= 0.183 Angle : 0.748 10.315 14545 Z= 0.390 Chirality : 0.047 0.302 1619 Planarity : 0.005 0.103 1845 Dihedral : 5.692 25.228 1457 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.36 % Favored : 93.41 % Rotamer: Outliers : 3.09 % Allowed : 26.53 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.96 (0.23), residues: 1325 helix: 0.55 (0.20), residues: 653 sheet: -0.57 (0.48), residues: 125 loop : -2.16 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 96 TYR 0.029 0.002 TYR d 177 PHE 0.022 0.002 PHE d 72 TRP 0.027 0.003 TRP E 108 HIS 0.013 0.002 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00420 (10765) covalent geometry : angle 0.74782 (14545) hydrogen bonds : bond 0.04053 ( 567) hydrogen bonds : angle 5.07228 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.02 seconds wall clock time: 44 minutes 26.32 seconds (2666.32 seconds total)