Starting phenix.real_space_refine on Mon Jul 28 16:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k26_36829/07_2025/8k26_36829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k26_36829/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k26_36829/07_2025/8k26_36829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k26_36829/07_2025/8k26_36829.map" model { file = "/net/cci-nas-00/data/ceres_data/8k26_36829/07_2025/8k26_36829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k26_36829/07_2025/8k26_36829.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'PHE:plan': 1, 'TRP: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, 'PHE:plan': 1, 'TRP: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: 14.58, per 1000 atoms: 1.38 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: 2.53 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.39 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: 4.73 Time building geometry restraints manager: 3.04 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: 27.470 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.890 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.065 0.006 TRP E 108 HIS 0.021 0.003 HIS a 36 PHE 0.040 0.004 PHE e 226 TYR 0.050 0.003 TYR e 180 ARG 0.016 0.002 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.13869 ( 567) hydrogen bonds : angle 7.22819 ( 1644) covalent geometry : bond 0.00636 (10765) covalent geometry : angle 1.30930 (14545) *********************** 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 : 1.074 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: 0.2546 time to fit residues: 55.5017 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 : 1.675 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.5174 r_free = 0.5174 target = 0.198577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.148815 restraints weight = 71599.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.160671 restraints weight = 22616.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.165691 restraints weight = 11874.802| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4773 r_free = 0.4773 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4774 r_free = 0.4774 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10765 Z= 0.178 Angle : 0.731 7.190 14545 Z= 0.390 Chirality : 0.046 0.166 1619 Planarity : 0.005 0.108 1845 Dihedral : 6.390 40.523 1463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 3.36 % Allowed : 27.94 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1325 helix: -0.52 (0.19), residues: 675 sheet: -0.46 (0.47), residues: 126 loop : -2.22 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP e 73 HIS 0.009 0.001 HIS D 132 PHE 0.026 0.002 PHE d 72 TYR 0.019 0.002 TYR E 284 ARG 0.009 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 567) hydrogen bonds : angle 5.14737 ( 1644) covalent geometry : bond 0.00405 (10765) covalent geometry : angle 0.73126 (14545) *********************** 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 178 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6983 (p90) cc_final: 0.5721 (p90) REVERT: D 141 GLU cc_start: 0.0407 (OUTLIER) cc_final: 0.0049 (mt-10) REVERT: D 204 LEU cc_start: 0.6499 (tp) cc_final: 0.5899 (tt) REVERT: D 207 TYR cc_start: 0.6918 (m-10) cc_final: 0.6598 (m-10) REVERT: E 61 MET cc_start: 0.3912 (mtm) cc_final: 0.3206 (mpp) REVERT: E 81 MET cc_start: 0.8518 (tmm) cc_final: 0.8290 (tmm) REVERT: d 124 MET cc_start: 0.1834 (ptp) cc_final: 0.1474 (ptt) REVERT: d 141 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.2796 (pp20) REVERT: d 294 MET cc_start: -0.1727 (OUTLIER) cc_final: -0.1939 (mtp) REVERT: A 24 TYR cc_start: 0.7438 (m-80) cc_final: 0.7027 (m-80) REVERT: a 4 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.4547 (ttp80) outliers start: 38 outliers final: 15 residues processed: 169 average time/residue: 0.2238 time to fit residues: 54.3150 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 50 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 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 112 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** d 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 230 HIS ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 192 HIS e 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.185898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.139513 restraints weight = 77553.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.149517 restraints weight = 26406.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.151755 restraints weight = 13843.268| |-----------------------------------------------------------------------------| r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4557 r_free = 0.4557 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4557 r_free = 0.4557 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 10765 Z= 0.337 Angle : 0.895 9.560 14545 Z= 0.484 Chirality : 0.052 0.198 1619 Planarity : 0.006 0.107 1845 Dihedral : 6.732 28.746 1457 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 28.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.59 % Favored : 93.18 % Rotamer: Outliers : 4.16 % Allowed : 27.50 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1325 helix: -0.54 (0.19), residues: 678 sheet: -0.85 (0.46), residues: 126 loop : -2.52 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP e 108 HIS 0.013 0.003 HIS D 30 PHE 0.037 0.003 PHE e 72 TYR 0.026 0.003 TYR A 27 ARG 0.006 0.001 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.05638 ( 567) hydrogen bonds : angle 5.80485 ( 1644) covalent geometry : bond 0.00769 (10765) covalent geometry : angle 0.89500 (14545) *********************** 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 178 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6405 (tp) cc_final: 0.5905 (tt) REVERT: D 207 TYR cc_start: 0.7336 (m-10) cc_final: 0.7109 (m-10) REVERT: D 245 ILE cc_start: 0.5963 (mm) cc_final: 0.5719 (mm) REVERT: d 108 TRP cc_start: 0.5724 (t60) cc_final: 0.5422 (t60) REVERT: d 226 PHE cc_start: 0.4715 (OUTLIER) cc_final: 0.4178 (m-80) REVERT: d 294 MET cc_start: -0.1639 (OUTLIER) cc_final: -0.1918 (mtp) REVERT: A 19 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7399 (tpt-90) REVERT: A 24 TYR cc_start: 0.7760 (m-80) cc_final: 0.7545 (m-80) REVERT: A 30 ASN cc_start: 0.6945 (t0) cc_final: 0.6436 (t0) REVERT: a 4 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.4753 (ttp-170) outliers start: 47 outliers final: 26 residues processed: 165 average time/residue: 0.2147 time to fit residues: 51.4104 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 : 1.178 ------------------------------------------------------------------------------- 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 252 LEU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain d residue 28 VAL 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 226 PHE 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 40 VAL Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE 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 58 VAL Chi-restraints excluded: chain a residue 3 ILE Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 60 CYS 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 36 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN d 12 ASN ** d 58 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 31 ASN A 61 ASN a 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.192785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.148066 restraints weight = 83381.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.157929 restraints weight = 28419.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.161681 restraints weight = 12580.374| |-----------------------------------------------------------------------------| r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 10765 Z= 0.162 Angle : 0.703 8.390 14545 Z= 0.373 Chirality : 0.046 0.177 1619 Planarity : 0.005 0.106 1845 Dihedral : 6.062 24.465 1457 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.17 % Rotamer: Outliers : 3.36 % Allowed : 27.76 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1325 helix: 0.02 (0.19), residues: 674 sheet: -0.56 (0.47), residues: 123 loop : -2.40 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP d 104 HIS 0.010 0.002 HIS d 230 PHE 0.019 0.002 PHE d 72 TYR 0.022 0.002 TYR E 207 ARG 0.005 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 567) hydrogen bonds : angle 5.22734 ( 1644) covalent geometry : bond 0.00376 (10765) covalent geometry : angle 0.70340 (14545) *********************** 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: 38 poor density : 133 time to evaluate : 1.192 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: 0.6592 (tp) cc_final: 0.6224 (tt) REVERT: D 207 TYR cc_start: 0.6991 (m-10) cc_final: 0.6662 (m-10) REVERT: D 245 ILE cc_start: 0.6077 (mm) cc_final: 0.5860 (mm) REVERT: D 252 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6349 (tt) REVERT: d 124 MET cc_start: 0.2728 (ptp) cc_final: 0.2039 (ptt) REVERT: d 294 MET cc_start: -0.1409 (OUTLIER) cc_final: -0.1740 (mtp) REVERT: e 101 MET cc_start: 0.5392 (mmm) cc_final: 0.3399 (tpt) REVERT: e 217 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 19 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7389 (tpt-90) REVERT: A 20 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 36 HIS cc_start: 0.5607 (OUTLIER) cc_final: 0.5359 (m-70) REVERT: a 4 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.4776 (ttp80) REVERT: a 65 LYS cc_start: 0.2145 (OUTLIER) cc_final: 0.1663 (pttt) outliers start: 38 outliers final: 20 residues processed: 161 average time/residue: 0.2367 time to fit residues: 54.2294 Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 144 ARG Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 217 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN d 58 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.193653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.144602 restraints weight = 78064.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.155960 restraints weight = 25033.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.163006 restraints weight = 11585.244| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4759 r_free = 0.4759 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 = 0.4759 r_free = 0.4759 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10765 Z= 0.147 Angle : 0.684 8.479 14545 Z= 0.359 Chirality : 0.046 0.231 1619 Planarity : 0.005 0.106 1845 Dihedral : 5.759 25.744 1457 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.45 % Favored : 94.32 % Rotamer: Outliers : 3.98 % Allowed : 27.06 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1325 helix: 0.36 (0.20), residues: 663 sheet: -0.47 (0.46), residues: 126 loop : -2.35 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 108 HIS 0.006 0.001 HIS d 30 PHE 0.020 0.002 PHE d 72 TYR 0.015 0.002 TYR E 207 ARG 0.005 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 567) hydrogen bonds : angle 5.00370 ( 1644) covalent geometry : bond 0.00341 (10765) covalent geometry : angle 0.68396 (14545) *********************** 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 180 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.353 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 141 GLU cc_start: 0.0205 (OUTLIER) cc_final: -0.0286 (mt-10) REVERT: D 204 LEU cc_start: 0.6288 (tp) cc_final: 0.5977 (tt) REVERT: E 132 HIS cc_start: 0.5047 (m-70) cc_final: 0.4559 (t-90) REVERT: E 294 MET cc_start: 0.6587 (ptp) cc_final: 0.6312 (ptp) REVERT: d 1 MET cc_start: 0.3900 (pmm) cc_final: 0.2787 (ttt) REVERT: d 13 MET cc_start: 0.7680 (mtm) cc_final: 0.7094 (mtm) REVERT: d 136 PHE cc_start: 0.2703 (OUTLIER) cc_final: 0.2137 (p90) REVERT: d 215 SER cc_start: 0.2393 (OUTLIER) cc_final: 0.1557 (t) REVERT: e 101 MET cc_start: 0.5726 (mmm) cc_final: 0.3945 (tpt) REVERT: e 217 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8254 (mm) REVERT: a 4 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.4891 (ttp80) REVERT: a 65 LYS cc_start: 0.2410 (OUTLIER) cc_final: 0.1962 (pttt) outliers start: 45 outliers final: 17 residues processed: 171 average time/residue: 0.2336 time to fit residues: 56.4541 Evaluate side-chains 147 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain D residue 272 CYS 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 215 SER Chi-restraints excluded: chain d residue 261 GLN 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 217 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 34 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** D 288 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 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.194600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.146401 restraints weight = 62814.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.158903 restraints weight = 21415.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.161708 restraints weight = 11290.029| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10765 Z= 0.141 Angle : 0.681 8.780 14545 Z= 0.355 Chirality : 0.045 0.265 1619 Planarity : 0.004 0.103 1845 Dihedral : 5.630 24.413 1457 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.17 % Rotamer: Outliers : 3.27 % Allowed : 27.23 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1325 helix: 0.52 (0.20), residues: 663 sheet: -0.29 (0.47), residues: 127 loop : -2.28 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 108 HIS 0.008 0.001 HIS A 36 PHE 0.019 0.002 PHE d 72 TYR 0.020 0.002 TYR a 84 ARG 0.006 0.001 ARG d 270 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 567) hydrogen bonds : angle 4.89734 ( 1644) covalent geometry : bond 0.00329 (10765) covalent geometry : angle 0.68118 (14545) *********************** 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 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7673 (mtm110) REVERT: D 141 GLU cc_start: 0.0183 (OUTLIER) cc_final: -0.0320 (mt-10) REVERT: D 204 LEU cc_start: 0.6297 (tp) cc_final: 0.5975 (tt) REVERT: E 132 HIS cc_start: 0.5236 (m-70) cc_final: 0.4696 (t-90) REVERT: E 294 MET cc_start: 0.6467 (ptp) cc_final: 0.6149 (ptp) REVERT: d 1 MET cc_start: 0.4496 (pmm) cc_final: 0.3432 (ttt) REVERT: d 136 PHE cc_start: 0.2923 (OUTLIER) cc_final: 0.2368 (p90) REVERT: d 252 LEU cc_start: -0.2907 (OUTLIER) cc_final: -0.3170 (tp) REVERT: d 263 MET cc_start: 0.6869 (pmm) cc_final: 0.6153 (pmm) REVERT: e 101 MET cc_start: 0.5732 (mmm) cc_final: 0.4003 (tpt) REVERT: a 65 LYS cc_start: 0.2630 (OUTLIER) cc_final: 0.2119 (pttt) outliers start: 37 outliers final: 19 residues processed: 156 average time/residue: 0.2523 time to fit residues: 58.1806 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain E residue 61 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 252 LEU Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 230 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN d 92 GLN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** 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 = 0.5102 r_free = 0.5102 target = 0.189974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.143293 restraints weight = 59222.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.153382 restraints weight = 20273.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.156659 restraints weight = 10583.915| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4667 r_free = 0.4667 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4667 r_free = 0.4667 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 10765 Z= 0.202 Angle : 0.742 8.833 14545 Z= 0.390 Chirality : 0.047 0.294 1619 Planarity : 0.005 0.103 1845 Dihedral : 5.791 25.396 1457 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.67 % Favored : 93.11 % Rotamer: Outliers : 3.09 % Allowed : 28.03 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1325 helix: 0.28 (0.19), residues: 672 sheet: -0.87 (0.44), residues: 144 loop : -2.29 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP d 218 HIS 0.016 0.002 HIS e 257 PHE 0.026 0.002 PHE e 72 TYR 0.015 0.002 TYR d 210 ARG 0.006 0.001 ARG d 270 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 567) hydrogen bonds : angle 5.17695 ( 1644) covalent geometry : bond 0.00472 (10765) covalent geometry : angle 0.74201 (14545) *********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 GLU cc_start: 0.0293 (OUTLIER) cc_final: -0.0217 (mt-10) REVERT: D 204 LEU cc_start: 0.6226 (tp) cc_final: 0.5881 (tt) REVERT: E 132 HIS cc_start: 0.5258 (m-70) cc_final: 0.4679 (t-90) REVERT: E 294 MET cc_start: 0.6510 (ptp) cc_final: 0.6255 (ptp) REVERT: d 1 MET cc_start: 0.4129 (pmm) cc_final: 0.3167 (ttt) REVERT: d 13 MET cc_start: 0.7817 (mtm) cc_final: 0.7293 (mtm) REVERT: d 136 PHE cc_start: 0.3087 (OUTLIER) cc_final: 0.2228 (p90) REVERT: d 215 SER cc_start: 0.2609 (OUTLIER) cc_final: 0.1993 (t) REVERT: d 263 MET cc_start: 0.6822 (pmm) cc_final: 0.6038 (pmm) REVERT: e 101 MET cc_start: 0.5705 (mmm) cc_final: 0.3707 (tpt) REVERT: e 178 LYS cc_start: 0.9075 (pttp) cc_final: 0.8403 (ptmm) REVERT: A 20 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 24 TYR cc_start: 0.7730 (m-80) cc_final: 0.7407 (m-80) REVERT: a 65 LYS cc_start: 0.2545 (OUTLIER) cc_final: 0.2063 (pttt) outliers start: 35 outliers final: 22 residues processed: 150 average time/residue: 0.3178 time to fit residues: 72.4329 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 201 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain d residue 33 GLU 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 215 SER Chi-restraints excluded: chain d residue 230 HIS 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 230 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.198865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.156303 restraints weight = 49558.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.166975 restraints weight = 21357.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.169804 restraints weight = 12315.873| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4736 r_free = 0.4736 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 = 0.4736 r_free = 0.4736 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10765 Z= 0.141 Angle : 0.705 10.218 14545 Z= 0.366 Chirality : 0.046 0.286 1619 Planarity : 0.004 0.103 1845 Dihedral : 5.558 23.735 1457 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.76 % Favored : 94.02 % Rotamer: Outliers : 2.74 % Allowed : 28.47 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1325 helix: 0.46 (0.19), residues: 667 sheet: -0.68 (0.44), residues: 145 loop : -2.21 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 104 HIS 0.017 0.002 HIS e 257 PHE 0.019 0.002 PHE d 72 TYR 0.021 0.002 TYR D 42 ARG 0.006 0.001 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 567) hydrogen bonds : angle 4.97627 ( 1644) covalent geometry : bond 0.00324 (10765) covalent geometry : angle 0.70488 (14545) *********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7665 (mtm110) REVERT: D 141 GLU cc_start: 0.0403 (OUTLIER) cc_final: -0.0138 (mt-10) REVERT: D 204 LEU cc_start: 0.6319 (tp) cc_final: 0.5995 (tt) REVERT: E 132 HIS cc_start: 0.5071 (m-70) cc_final: 0.4610 (t-90) REVERT: d 1 MET cc_start: 0.4491 (pmm) cc_final: 0.3516 (ttt) REVERT: d 13 MET cc_start: 0.7679 (mtm) cc_final: 0.7113 (mtm) REVERT: d 136 PHE cc_start: 0.3209 (OUTLIER) cc_final: 0.2054 (p90) REVERT: d 215 SER cc_start: 0.2357 (OUTLIER) cc_final: 0.1792 (t) REVERT: d 263 MET cc_start: 0.6640 (pmm) cc_final: 0.5841 (pmm) REVERT: e 101 MET cc_start: 0.5562 (mmm) cc_final: 0.3840 (tpt) REVERT: e 178 LYS cc_start: 0.9013 (pttp) cc_final: 0.8380 (ptmm) REVERT: A 24 TYR cc_start: 0.7361 (m-80) cc_final: 0.7057 (m-80) REVERT: a 65 LYS cc_start: 0.2935 (OUTLIER) cc_final: 0.2408 (pttt) outliers start: 31 outliers final: 22 residues processed: 150 average time/residue: 0.2309 time to fit residues: 52.3220 Evaluate side-chains 145 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 33 GLU 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 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 230 HIS 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 80 SER 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 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 57 optimal weight: 0.0370 chunk 106 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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 288 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 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.198988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.162949 restraints weight = 80125.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.169939 restraints weight = 44092.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.176305 restraints weight = 17337.748| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4834 r_free = 0.4834 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4834 r_free = 0.4834 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10765 Z= 0.142 Angle : 0.700 9.288 14545 Z= 0.364 Chirality : 0.046 0.291 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.441 23.387 1457 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.94 % Rotamer: Outliers : 2.83 % Allowed : 28.21 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1325 helix: 0.54 (0.19), residues: 667 sheet: -0.33 (0.48), residues: 125 loop : -2.20 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 104 HIS 0.008 0.001 HIS A 36 PHE 0.019 0.002 PHE d 72 TYR 0.019 0.002 TYR d 177 ARG 0.006 0.001 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 567) hydrogen bonds : angle 4.89238 ( 1644) covalent geometry : bond 0.00330 (10765) covalent geometry : angle 0.70037 (14545) *********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6608 (tp) cc_final: 0.6254 (tt) REVERT: d 1 MET cc_start: 0.4705 (pmm) cc_final: 0.3766 (ttt) REVERT: d 13 MET cc_start: 0.7624 (mtm) cc_final: 0.7135 (mtm) REVERT: d 136 PHE cc_start: 0.3648 (OUTLIER) cc_final: 0.2301 (p90) REVERT: d 215 SER cc_start: 0.2333 (OUTLIER) cc_final: 0.1723 (t) REVERT: d 263 MET cc_start: 0.6535 (pmm) cc_final: 0.5808 (pmm) REVERT: e 101 MET cc_start: 0.5380 (mmm) cc_final: 0.3674 (tpt) REVERT: e 178 LYS cc_start: 0.8619 (pttp) cc_final: 0.8253 (pttm) REVERT: A 24 TYR cc_start: 0.7344 (m-80) cc_final: 0.7105 (m-80) REVERT: a 65 LYS cc_start: 0.2775 (OUTLIER) cc_final: 0.2291 (pttt) outliers start: 32 outliers final: 23 residues processed: 150 average time/residue: 0.2028 time to fit residues: 45.1786 Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain d residue 33 GLU 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 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 230 HIS 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 80 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 0.0770 chunk 99 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** 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 ** 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 = 0.5156 r_free = 0.5156 target = 0.198826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.155068 restraints weight = 56563.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.165543 restraints weight = 23600.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.168624 restraints weight = 13702.943| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4719 r_free = 0.4719 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4719 r_free = 0.4719 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.4719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10765 Z= 0.146 Angle : 0.703 9.742 14545 Z= 0.365 Chirality : 0.045 0.296 1619 Planarity : 0.004 0.101 1845 Dihedral : 5.397 23.311 1457 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.17 % Rotamer: Outliers : 2.39 % Allowed : 28.47 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1325 helix: 0.59 (0.20), residues: 669 sheet: -0.76 (0.44), residues: 145 loop : -2.17 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 104 HIS 0.008 0.001 HIS A 36 PHE 0.020 0.002 PHE d 72 TYR 0.018 0.002 TYR d 177 ARG 0.009 0.001 ARG d 270 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 567) hydrogen bonds : angle 4.85660 ( 1644) covalent geometry : bond 0.00341 (10765) covalent geometry : angle 0.70250 (14545) ********************** 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 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 HIS cc_start: 0.6957 (m90) cc_final: 0.6718 (m-70) REVERT: D 204 LEU cc_start: 0.6477 (tp) cc_final: 0.6144 (tt) REVERT: E 132 HIS cc_start: 0.4995 (t-90) cc_final: 0.4726 (t-170) REVERT: d 1 MET cc_start: 0.4736 (pmm) cc_final: 0.3876 (ttt) REVERT: d 13 MET cc_start: 0.7690 (mtm) cc_final: 0.7124 (mtm) REVERT: d 136 PHE cc_start: 0.3505 (OUTLIER) cc_final: 0.2143 (p90) REVERT: d 215 SER cc_start: 0.2422 (OUTLIER) cc_final: 0.1855 (t) REVERT: d 263 MET cc_start: 0.6567 (pmm) cc_final: 0.5814 (pmm) REVERT: e 101 MET cc_start: 0.5505 (mmm) cc_final: 0.3765 (tpt) REVERT: e 178 LYS cc_start: 0.8986 (pttp) cc_final: 0.8630 (pttm) REVERT: a 65 LYS cc_start: 0.3023 (OUTLIER) cc_final: 0.2476 (pttt) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.3359 time to fit residues: 73.2951 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain d residue 33 GLU 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 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 230 HIS 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 80 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 40.0000 overall best weight: 1.5282 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 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 = 0.5119 r_free = 0.5119 target = 0.191784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.142718 restraints weight = 66688.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.154479 restraints weight = 22879.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.158185 restraints weight = 12112.242| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 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 = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.4674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.4888 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= 0.159 Angle : 0.716 10.762 14545 Z= 0.371 Chirality : 0.046 0.309 1619 Planarity : 0.004 0.101 1845 Dihedral : 5.434 23.711 1457 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.98 % Favored : 93.79 % Rotamer: Outliers : 2.30 % Allowed : 28.38 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1325 helix: 0.63 (0.20), residues: 665 sheet: -0.90 (0.44), residues: 145 loop : -2.26 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP d 218 HIS 0.008 0.001 HIS A 36 PHE 0.021 0.002 PHE d 72 TYR 0.018 0.002 TYR d 210 ARG 0.008 0.001 ARG d 270 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 567) hydrogen bonds : angle 4.91309 ( 1644) covalent geometry : bond 0.00372 (10765) covalent geometry : angle 0.71577 (14545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5385.21 seconds wall clock time: 99 minutes 2.11 seconds (5942.11 seconds total)