Starting phenix.real_space_refine on Sun Dec 29 22:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.map" model { file = "/net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k21_36824/12_2024/8k21_36824.cif" } resolution = 3.8 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 468 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 63 5.16 5 C 7148 2.51 5 N 1947 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11389 Number of models: 1 Model: "" Number of chains: 8 Chain: "U" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "V" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 583 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 2327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2317 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 295, 2322 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 2358 Chain: "E" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2353 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 5, 'TRANS': 289} Chain: "a" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 571 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 2360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2350 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 295, 2350 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2388 Chain: "e" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2337 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 9.60, per 1000 atoms: 0.84 Number of scatterers: 11389 At special positions: 0 Unit cell: (107.8, 119.9, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 41 15.00 O 2190 8.00 N 1947 7.00 C 7148 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: 3.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 53.7% alpha, 9.7% beta 15 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 4.148A pdb=" N LYS A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 100 through 110 removed outlier: 4.200A pdb=" N ARG D 106 " --> pdb=" O GLN D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.656A pdb=" N GLN D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 184 Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 243 through 248 removed outlier: 3.968A pdb=" N THR D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.556A pdb=" N VAL D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D 276 " --> pdb=" O CYS D 272 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.928A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 98 through 109 Processing helix chain 'E' and resid 110 through 123 Processing helix chain 'E' and resid 123 through 132 removed outlier: 4.457A pdb=" N ASP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.622A pdb=" N SER E 146 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 184 removed outlier: 3.704A pdb=" N LYS E 178 " --> pdb=" O LYS E 174 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR E 184 " --> pdb=" O TYR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 219 removed outlier: 3.602A pdb=" N ILE E 212 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.648A pdb=" N PHE E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 4.022A 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 removed outlier: 3.797A pdb=" N ASN E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'a' and resid 10 through 22 removed outlier: 4.447A pdb=" N LYS a 16 " --> pdb=" O PRO a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'd' and resid 6 through 10 Processing helix chain 'd' and resid 58 through 68 Processing helix chain 'd' and resid 100 through 110 removed outlier: 4.280A pdb=" N ARG d 106 " --> pdb=" O GLN d 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP d 110 " --> pdb=" O ARG d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 132 removed outlier: 4.538A pdb=" N ARG d 125 " --> pdb=" O ILE d 121 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL d 126 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER d 130 " --> pdb=" O VAL d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 143 through 158 Processing helix chain 'd' and resid 161 through 184 Processing helix chain 'd' and resid 196 through 221 Processing helix chain 'd' and resid 238 through 243 Processing helix chain 'd' and resid 244 through 249 removed outlier: 3.760A pdb=" N SER d 249 " --> pdb=" O ILE d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 261 removed outlier: 3.636A pdb=" N LEU d 254 " --> pdb=" O ILE d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 279 Processing helix chain 'd' and resid 280 through 294 removed outlier: 3.568A pdb=" N LYS d 290 " --> pdb=" O ILE d 286 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG d 291 " --> pdb=" O ASN d 287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU d 292 " --> pdb=" O ASN d 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 68 removed outlier: 3.672A pdb=" N MET e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA e 66 " --> pdb=" O SER e 62 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY e 68 " --> pdb=" O LEU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 110 removed outlier: 3.541A pdb=" N ASN e 103 " --> pdb=" O LYS e 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP e 104 " --> pdb=" O TYR e 100 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP e 110 " --> pdb=" O ARG e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 132 removed outlier: 4.057A pdb=" N VAL e 126 " --> pdb=" O LEU e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 157 removed outlier: 3.932A pdb=" N ILE e 148 " --> pdb=" O ARG e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 184 Processing helix chain 'e' and resid 196 through 221 removed outlier: 3.682A pdb=" N TYR e 208 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA e 213 " --> pdb=" O ALA e 209 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 244 removed outlier: 4.171A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (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 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.868A pdb=" N TYR D 14 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA E 83 " --> pdb=" O TRP E 73 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN E 12 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY E 49 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR E 14 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 37 through 40 removed outlier: 4.574A pdb=" N VAL D 28 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER D 55 " --> pdb=" O CYS D 19 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 23 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 56 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 21 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 24 removed outlier: 3.585A pdb=" N GLN E 27 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.720A pdb=" N ARG a 4 " --> pdb=" O ASN a 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL a 58 " --> pdb=" O ALA a 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA a 69 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS a 60 " --> pdb=" O LEU a 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 21 through 24 removed outlier: 3.503A pdb=" N GLN d 27 " --> pdb=" O LYS d 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 47 through 50 removed outlier: 3.673A pdb=" N PHE d 72 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA e 83 " --> pdb=" O TRP e 73 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE e 48 " --> pdb=" O PHE e 72 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR e 74 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU e 50 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR e 14 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET e 13 " --> pdb=" O ILE e 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 55 through 57 removed outlier: 3.605A pdb=" N SER e 55 " --> pdb=" O CYS e 19 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR e 57 " --> pdb=" O VAL e 21 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL e 23 " --> pdb=" O THR e 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS e 30 " --> pdb=" O TYR e 38 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1804 1.31 - 1.44: 3432 1.44 - 1.56: 6286 1.56 - 1.69: 87 1.69 - 1.82: 102 Bond restraints: 11711 Sorted by residual: bond pdb=" N PHE d 226 " pdb=" CA PHE d 226 " ideal model delta sigma weight residual 1.464 1.378 0.085 1.09e-02 8.42e+03 6.10e+01 bond pdb=" CA ASN d 224 " pdb=" C ASN d 224 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.32e-02 5.74e+03 5.86e+01 bond pdb=" CA ALA d 219 " pdb=" C ALA d 219 " ideal model delta sigma weight residual 1.522 1.420 0.102 1.40e-02 5.10e+03 5.32e+01 bond pdb=" CA ALA D 118 " pdb=" C ALA D 118 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.29e-02 6.01e+03 5.29e+01 bond pdb=" CA VAL d 239 " pdb=" C VAL d 239 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.22e-02 6.72e+03 5.07e+01 ... (remaining 11706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 15336 2.83 - 5.66: 525 5.66 - 8.49: 114 8.49 - 11.32: 19 11.32 - 14.15: 6 Bond angle restraints: 16000 Sorted by residual: angle pdb=" N ALA D 118 " pdb=" CA ALA D 118 " pdb=" C ALA D 118 " ideal model delta sigma weight residual 111.36 99.78 11.58 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N ASN d 224 " pdb=" CA ASN d 224 " pdb=" C ASN d 224 " ideal model delta sigma weight residual 113.50 101.30 12.20 1.23e+00 6.61e-01 9.83e+01 angle pdb=" N LEU d 238 " pdb=" CA LEU d 238 " pdb=" C LEU d 238 " ideal model delta sigma weight residual 113.23 102.53 10.70 1.24e+00 6.50e-01 7.45e+01 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 111.90 105.24 6.66 8.10e-01 1.52e+00 6.76e+01 angle pdb=" N HIS E 257 " pdb=" CA HIS E 257 " pdb=" C HIS E 257 " ideal model delta sigma weight residual 112.23 102.12 10.11 1.26e+00 6.30e-01 6.44e+01 ... (remaining 15995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5283 17.94 - 35.89: 985 35.89 - 53.83: 454 53.83 - 71.77: 107 71.77 - 89.71: 24 Dihedral angle restraints: 6853 sinusoidal: 2972 harmonic: 3881 Sorted by residual: dihedral pdb=" CA THR e 45 " pdb=" C THR e 45 " pdb=" N VAL e 46 " pdb=" CA VAL e 46 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER d 175 " pdb=" C SER d 175 " pdb=" N LEU d 176 " pdb=" CA LEU d 176 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE E 188 " pdb=" C PHE E 188 " pdb=" N LYS E 189 " pdb=" CA LYS E 189 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1498 0.097 - 0.194: 228 0.194 - 0.291: 42 0.291 - 0.388: 12 0.388 - 0.485: 2 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB ILE D 245 " pdb=" CA ILE D 245 " pdb=" CG1 ILE D 245 " pdb=" CG2 ILE D 245 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CB VAL e 105 " pdb=" CA VAL e 105 " pdb=" CG1 VAL e 105 " pdb=" CG2 VAL e 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA ILE d 251 " pdb=" N ILE d 251 " pdb=" C ILE d 251 " pdb=" CB ILE d 251 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1779 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 255 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ALA E 255 " 0.089 2.00e-02 2.50e+03 pdb=" O ALA E 255 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE E 256 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 209 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ALA d 209 " 0.081 2.00e-02 2.50e+03 pdb=" O ALA d 209 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR d 210 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 268 " 0.024 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE E 268 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE E 268 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 268 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 268 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 268 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 268 " 0.003 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2126 2.77 - 3.30: 10428 3.30 - 3.83: 21040 3.83 - 4.37: 24563 4.37 - 4.90: 39521 Nonbonded interactions: 97678 Sorted by model distance: nonbonded pdb=" O THR d 171 " pdb=" OG SER d 175 " model vdw 2.232 3.040 nonbonded pdb=" O ASP e 153 " pdb=" OG1 THR e 157 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP d 127 " pdb=" OH TYR d 284 " model vdw 2.252 3.040 nonbonded pdb=" O ASP d 153 " pdb=" OG1 THR d 157 " model vdw 2.258 3.040 nonbonded pdb=" O SER D 225 " pdb=" OG SER D 225 " model vdw 2.264 3.040 ... (remaining 97673 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 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 14 or (resid 15 and (name \ N or name CA or name C or name O or name CB )) or resid 16 through 75)) selection = chain 'a' } ncs_group { reference = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 141 or (resid 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 through 149 or \ resid 151 through 234 or (resid 235 and (name N or name CA or name C or name O \ or name CB )) or resid 236 through 286 or resid 288 through 295)) selection = (chain 'E' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 141 or (resid 142 and (name N or name CA o \ r name C or name O or name CB )) or resid 143 through 149 or resid 151 through 2 \ 34 or (resid 235 and (name N or name CA or name C or name O or name CB )) or res \ id 236 through 286 or resid 288 through 295)) selection = (chain 'd' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 149 or resid 151 through 234 or (resid 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 2 \ 86 or resid 288 through 295)) selection = (chain 'e' and (resid 1 through 78 or (resid 79 through 84 and (name N or name C \ A or name C or name O or name CB )) or resid 85 through 110 or (resid 111 and (n \ ame N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 an \ d (name N or name CA or name C or name O or name CB )) or resid 114 through 118 \ or (resid 119 and (name N or name CA or name C or name O or name CB )) or resid \ 120 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 149 or resid 151 through 286 or resid 288 through 29 \ 5)) } 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=0.15 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.810 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.009 0.102 11711 Z= 0.580 Angle : 1.288 14.150 16000 Z= 0.783 Chirality : 0.079 0.485 1782 Planarity : 0.008 0.112 1878 Dihedral : 22.880 89.714 4367 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.91 % Favored : 92.48 % Rotamer: Outliers : 8.12 % Allowed : 36.28 % Favored : 55.60 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -3.31 (0.19), residues: 1321 helix: -1.77 (0.16), residues: 685 sheet: -1.71 (0.48), residues: 111 loop : -2.76 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP d 218 HIS 0.014 0.002 HIS D 30 PHE 0.064 0.004 PHE E 268 TYR 0.045 0.004 TYR d 100 ARG 0.016 0.001 ARG d 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 261 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7258 (tt0) cc_final: 0.6781 (tt0) REVERT: E 260 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: a 48 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8358 (mttp) REVERT: d 228 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8807 (tp) REVERT: e 61 MET cc_start: 0.8323 (ttm) cc_final: 0.7781 (ttm) outliers start: 91 outliers final: 15 residues processed: 322 average time/residue: 0.3108 time to fit residues: 132.6527 Evaluate side-chains 160 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain d residue 61 MET Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 27 GLN Chi-restraints excluded: chain e residue 242 VAL Chi-restraints excluded: chain e residue 294 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 ASN ** D 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 279 ASN E 9 GLN E 44 ASN E 132 HIS E 261 GLN a 72 ASN d 199 ASN e 27 GLN ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11711 Z= 0.277 Angle : 0.744 10.112 16000 Z= 0.402 Chirality : 0.045 0.174 1782 Planarity : 0.005 0.054 1878 Dihedral : 18.945 83.201 1955 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 5.21 % Allowed : 33.36 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.21), residues: 1321 helix: -0.34 (0.18), residues: 696 sheet: -1.44 (0.47), residues: 114 loop : -2.35 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP e 218 HIS 0.014 0.002 HIS D 192 PHE 0.024 0.002 PHE e 152 TYR 0.023 0.002 TYR d 284 ARG 0.009 0.001 ARG d 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7532 (tp-100) REVERT: D 202 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9134 (tp) REVERT: a 43 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8444 (p) REVERT: e 30 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.5876 (m170) REVERT: e 124 MET cc_start: 0.8269 (ptp) cc_final: 0.8066 (ptp) outliers start: 58 outliers final: 21 residues processed: 178 average time/residue: 0.2520 time to fit residues: 63.6294 Evaluate side-chains 135 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 153 ASP Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 266 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS E 4 GLN E 25 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN a 36 HIS ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 72 ASN d 89 HIS d 134 HIS ** d 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11711 Z= 0.269 Angle : 0.703 13.100 16000 Z= 0.374 Chirality : 0.044 0.220 1782 Planarity : 0.004 0.048 1878 Dihedral : 18.563 84.643 1922 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 4.06 % Allowed : 31.77 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.23), residues: 1321 helix: 0.35 (0.19), residues: 700 sheet: -1.89 (0.43), residues: 136 loop : -2.03 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 218 HIS 0.007 0.001 HIS e 168 PHE 0.024 0.002 PHE E 276 TYR 0.018 0.002 TYR d 284 ARG 0.007 0.001 ARG d 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 202 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9156 (tp) REVERT: a 43 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8453 (p) REVERT: d 64 LEU cc_start: 0.9355 (mt) cc_final: 0.9138 (mp) REVERT: d 158 GLN cc_start: 0.8147 (pp30) cc_final: 0.7865 (pp30) REVERT: e 22 LEU cc_start: 0.8727 (tp) cc_final: 0.8414 (tt) REVERT: e 30 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5931 (m170) outliers start: 45 outliers final: 22 residues processed: 148 average time/residue: 0.2429 time to fit residues: 51.8405 Evaluate side-chains 126 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 ASN D 150 ASN B D 158 GLN D 287 ASN B ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS a 72 ASN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11711 Z= 0.229 Angle : 0.685 13.491 16000 Z= 0.356 Chirality : 0.044 0.269 1782 Planarity : 0.004 0.047 1878 Dihedral : 18.458 84.328 1920 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.76 % Rotamer: Outliers : 3.71 % Allowed : 30.63 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.23), residues: 1321 helix: 0.71 (0.20), residues: 704 sheet: -1.73 (0.44), residues: 136 loop : -2.05 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 73 HIS 0.007 0.001 HIS d 168 PHE 0.022 0.002 PHE A 68 TYR 0.015 0.001 TYR d 284 ARG 0.008 0.001 ARG e 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 MET cc_start: 0.8539 (mmm) cc_final: 0.8289 (mmm) REVERT: D 202 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9132 (tp) REVERT: a 43 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8620 (p) REVERT: d 158 GLN cc_start: 0.8161 (pp30) cc_final: 0.7932 (pp30) REVERT: e 22 LEU cc_start: 0.8728 (tp) cc_final: 0.8464 (tt) outliers start: 41 outliers final: 23 residues processed: 141 average time/residue: 0.2574 time to fit residues: 52.1865 Evaluate side-chains 118 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.0010 chunk 89 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 25 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 58 ASN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11711 Z= 0.199 Angle : 0.668 13.788 16000 Z= 0.345 Chirality : 0.043 0.268 1782 Planarity : 0.004 0.049 1878 Dihedral : 18.303 83.539 1917 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 3.35 % Allowed : 30.19 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.23), residues: 1321 helix: 0.86 (0.20), residues: 704 sheet: -1.82 (0.49), residues: 112 loop : -2.04 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 73 HIS 0.006 0.001 HIS d 168 PHE 0.020 0.002 PHE A 68 TYR 0.014 0.001 TYR e 100 ARG 0.007 0.001 ARG e 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 1.304 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: A 40 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7686 (tp-100) REVERT: D 202 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9119 (tp) REVERT: E 63 MET cc_start: 0.7717 (ppp) cc_final: 0.7515 (ppp) REVERT: a 43 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8540 (p) REVERT: d 158 GLN cc_start: 0.8206 (pp30) cc_final: 0.7992 (pp30) REVERT: e 30 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.5976 (m170) REVERT: e 264 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8030 (p) outliers start: 37 outliers final: 17 residues processed: 139 average time/residue: 0.2421 time to fit residues: 48.4506 Evaluate side-chains 117 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 264 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 150 ASN B ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 GLN ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11711 Z= 0.191 Angle : 0.685 19.116 16000 Z= 0.347 Chirality : 0.043 0.226 1782 Planarity : 0.004 0.048 1878 Dihedral : 18.180 81.917 1916 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 2.03 % Allowed : 31.33 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.23), residues: 1321 helix: 1.00 (0.20), residues: 701 sheet: -1.53 (0.47), residues: 134 loop : -1.92 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.020 0.002 PHE E 152 TYR 0.017 0.001 TYR d 275 ARG 0.010 0.001 ARG e 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7662 (tp-100) REVERT: A 75 MET cc_start: 0.6076 (tpt) cc_final: 0.5797 (tpt) REVERT: D 202 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9098 (tp) REVERT: E 263 MET cc_start: 0.8478 (pmm) cc_final: 0.7880 (pmm) REVERT: a 43 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8351 (p) REVERT: a 75 MET cc_start: 0.7845 (tmm) cc_final: 0.7346 (tmm) REVERT: d 158 GLN cc_start: 0.8195 (pp30) cc_final: 0.7989 (pp30) outliers start: 22 outliers final: 14 residues processed: 126 average time/residue: 0.2508 time to fit residues: 45.7551 Evaluate side-chains 110 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain e residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11711 Z= 0.249 Angle : 0.708 18.907 16000 Z= 0.361 Chirality : 0.044 0.229 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.199 84.575 1916 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 2.47 % Allowed : 30.71 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.23), residues: 1321 helix: 1.13 (0.20), residues: 701 sheet: -1.58 (0.47), residues: 122 loop : -1.91 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.020 0.002 PHE A 68 TYR 0.014 0.001 TYR d 275 ARG 0.008 0.001 ARG e 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7809 (tp-100) REVERT: D 61 MET cc_start: 0.8884 (mmm) cc_final: 0.8601 (mmm) REVERT: D 202 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9147 (tp) REVERT: E 63 MET cc_start: 0.7674 (ppp) cc_final: 0.7444 (ppp) REVERT: a 43 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8389 (p) REVERT: d 61 MET cc_start: 0.8813 (mmm) cc_final: 0.8471 (mmm) REVERT: d 158 GLN cc_start: 0.8187 (pp30) cc_final: 0.7985 (pp30) REVERT: e 30 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6298 (m170) REVERT: e 124 MET cc_start: 0.8080 (ptp) cc_final: 0.7667 (ptp) outliers start: 27 outliers final: 19 residues processed: 114 average time/residue: 0.2398 time to fit residues: 40.4987 Evaluate side-chains 114 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 153 ASP Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11711 Z= 0.217 Angle : 0.711 18.859 16000 Z= 0.359 Chirality : 0.043 0.220 1782 Planarity : 0.004 0.044 1878 Dihedral : 18.135 86.378 1916 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 2.21 % Allowed : 31.07 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.23), residues: 1321 helix: 1.14 (0.20), residues: 699 sheet: -1.44 (0.48), residues: 122 loop : -1.84 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.020 0.002 PHE A 68 TYR 0.014 0.001 TYR e 100 ARG 0.015 0.001 ARG e 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.488 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: A 40 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7769 (tp-100) REVERT: D 61 MET cc_start: 0.8825 (mmm) cc_final: 0.8488 (mmm) REVERT: D 202 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9139 (tp) REVERT: E 63 MET cc_start: 0.7684 (ppp) cc_final: 0.7418 (ppp) REVERT: a 43 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8519 (p) REVERT: a 75 MET cc_start: 0.8025 (tmm) cc_final: 0.7592 (tmm) REVERT: d 158 GLN cc_start: 0.8182 (pp30) cc_final: 0.7972 (pp30) REVERT: e 248 THR cc_start: 0.8260 (p) cc_final: 0.8042 (t) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 0.2210 time to fit residues: 38.9169 Evaluate side-chains 110 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11711 Z= 0.204 Angle : 0.723 19.313 16000 Z= 0.363 Chirality : 0.043 0.219 1782 Planarity : 0.004 0.077 1878 Dihedral : 18.058 85.469 1916 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 1.77 % Allowed : 31.42 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.23), residues: 1321 helix: 1.20 (0.20), residues: 701 sheet: -1.31 (0.48), residues: 122 loop : -1.80 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.019 0.002 PHE E 152 TYR 0.013 0.001 TYR D 100 ARG 0.015 0.001 ARG A 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.178 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: A 40 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7736 (tp-100) REVERT: D 61 MET cc_start: 0.8845 (mmm) cc_final: 0.8580 (mmm) REVERT: D 202 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9119 (tp) REVERT: E 9 GLN cc_start: 0.6683 (mp10) cc_final: 0.6462 (mp10) REVERT: E 63 MET cc_start: 0.7699 (ppp) cc_final: 0.7443 (ppp) REVERT: a 43 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8541 (p) REVERT: a 75 MET cc_start: 0.8105 (tmm) cc_final: 0.7676 (tmm) REVERT: e 248 THR cc_start: 0.8213 (p) cc_final: 0.7992 (t) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.2327 time to fit residues: 38.7109 Evaluate side-chains 106 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0170 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11711 Z= 0.203 Angle : 0.737 19.711 16000 Z= 0.369 Chirality : 0.043 0.215 1782 Planarity : 0.004 0.068 1878 Dihedral : 18.031 85.335 1916 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 31.77 % Favored : 66.55 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.23), residues: 1321 helix: 1.19 (0.20), residues: 701 sheet: -1.18 (0.49), residues: 120 loop : -1.73 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.038 0.002 PHE a 2 TYR 0.012 0.001 TYR d 275 ARG 0.015 0.001 ARG A 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.318 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: A 40 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7722 (tp-100) REVERT: D 61 MET cc_start: 0.8806 (mmm) cc_final: 0.8538 (mmm) REVERT: D 202 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9118 (tp) REVERT: E 63 MET cc_start: 0.7711 (ppp) cc_final: 0.7453 (ppp) REVERT: a 43 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8486 (p) REVERT: a 75 MET cc_start: 0.8130 (tmm) cc_final: 0.7695 (tmm) REVERT: e 13 MET cc_start: 0.6953 (tpp) cc_final: 0.6474 (tpp) REVERT: e 248 THR cc_start: 0.8201 (p) cc_final: 0.7991 (t) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.2007 time to fit residues: 34.0610 Evaluate side-chains 110 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** 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 = 0.3111 r_free = 0.3111 target = 0.043238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033201 restraints weight = 117915.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034683 restraints weight = 52757.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.035711 restraints weight = 31954.200| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11711 Z= 0.206 Angle : 0.739 18.925 16000 Z= 0.371 Chirality : 0.043 0.221 1782 Planarity : 0.004 0.064 1878 Dihedral : 18.009 85.518 1916 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 1.94 % Allowed : 31.95 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.23), residues: 1321 helix: 1.11 (0.20), residues: 714 sheet: -1.19 (0.52), residues: 110 loop : -1.70 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 PHE 0.025 0.002 PHE E 152 TYR 0.012 0.001 TYR d 275 ARG 0.015 0.001 ARG A 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.36 seconds wall clock time: 42 minutes 5.67 seconds (2525.67 seconds total)