Starting phenix.real_space_refine on Fri Feb 14 18:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k26_36829/02_2025/8k26_36829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k26_36829/02_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_36829/02_2025/8k26_36829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k26_36829/02_2025/8k26_36829.map" model { file = "/net/cci-nas-00/data/ceres_data/8k26_36829/02_2025/8k26_36829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k26_36829/02_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-5592/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: 10.30, per 1000 atoms: 0.98 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: 2.31 Conformation dependent library (CDL) restraints added in 2.5 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: 1.05 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: 2.97 Time building geometry restraints manager: 2.74 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: 0.870 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.020 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- 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= 0.409 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 *********************** 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 : 1.181 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: 0.2496 time to fit residues: 53.8440 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 : 1.099 ------------------------------------------------------------------------------- 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 = 0.198578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.148813 restraints weight = 71598.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.160665 restraints weight = 22617.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.165695 restraints weight = 11865.371| |-----------------------------------------------------------------------------| 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= 0.252 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 *********************** 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 : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6985 (p90) cc_final: 0.5721 (p90) REVERT: D 141 GLU cc_start: 0.0408 (OUTLIER) cc_final: 0.0050 (mt-10) REVERT: D 204 LEU cc_start: 0.6501 (tp) cc_final: 0.5900 (tt) REVERT: D 207 TYR cc_start: 0.6919 (m-10) cc_final: 0.6598 (m-10) REVERT: E 61 MET cc_start: 0.3911 (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: 0.1833 (ptp) cc_final: 0.1473 (ptt) REVERT: d 141 GLU cc_start: 0.3304 (OUTLIER) cc_final: 0.2797 (pp20) REVERT: d 294 MET cc_start: -0.1731 (OUTLIER) cc_final: -0.1942 (mtp) REVERT: A 24 TYR cc_start: 0.7436 (m-80) cc_final: 0.7025 (m-80) REVERT: a 4 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.4546 (ttp80) outliers start: 38 outliers final: 15 residues processed: 169 average time/residue: 0.2384 time to fit residues: 57.3500 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 : 1.162 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.184267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.140606 restraints weight = 78346.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.147782 restraints weight = 28525.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.150696 restraints weight = 13618.078| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4562 r_free = 0.4562 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4561 r_free = 0.4561 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.143 10765 Z= 0.523 Angle : 0.935 10.139 14545 Z= 0.506 Chirality : 0.053 0.229 1619 Planarity : 0.007 0.113 1845 Dihedral : 6.919 29.784 1457 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 31.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.52 % Favored : 93.26 % Rotamer: Outliers : 4.24 % Allowed : 27.76 % Favored : 67.99 % 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: -2.07 (0.21), residues: 1325 helix: -0.59 (0.19), residues: 674 sheet: -0.88 (0.46), residues: 124 loop : -2.50 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP e 108 HIS 0.013 0.003 HIS D 30 PHE 0.039 0.004 PHE e 72 TYR 0.026 0.003 TYR A 27 ARG 0.006 0.001 ARG D 11 *********************** 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 177 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 LEU cc_start: 0.6533 (tp) cc_final: 0.6032 (tt) REVERT: D 207 TYR cc_start: 0.7390 (m-10) cc_final: 0.7171 (m-10) REVERT: D 245 ILE cc_start: 0.5781 (mm) cc_final: 0.5533 (mm) REVERT: d 45 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7943 (p) REVERT: d 108 TRP cc_start: 0.5442 (t60) cc_final: 0.5034 (t60) REVERT: d 226 PHE cc_start: 0.4768 (OUTLIER) cc_final: 0.4044 (m-80) REVERT: d 294 MET cc_start: -0.1425 (OUTLIER) cc_final: -0.1726 (mtp) REVERT: A 19 ARG cc_start: 0.7748 (mmm160) cc_final: 0.7416 (tpt-90) REVERT: A 30 ASN cc_start: 0.6942 (t0) cc_final: 0.6427 (t0) REVERT: a 4 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.4877 (ttp-170) outliers start: 48 outliers final: 25 residues processed: 165 average time/residue: 0.2282 time to fit residues: 54.6000 Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 122 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 GLN ** 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 E 224 ASN d 12 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN A 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.194654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.147534 restraints weight = 82464.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.158314 restraints weight = 27094.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.163478 restraints weight = 12245.413| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4760 r_free = 0.4760 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4761 r_free = 0.4761 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10765 Z= 0.194 Angle : 0.704 9.070 14545 Z= 0.370 Chirality : 0.046 0.203 1619 Planarity : 0.005 0.105 1845 Dihedral : 6.020 24.249 1457 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.08 % Favored : 94.70 % Rotamer: Outliers : 2.92 % Allowed : 27.50 % Favored : 69.58 % 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: -1.42 (0.22), residues: 1325 helix: 0.06 (0.19), residues: 669 sheet: -0.53 (0.47), residues: 123 loop : -2.37 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 104 HIS 0.007 0.001 HIS d 168 PHE 0.016 0.002 PHE E 152 TYR 0.023 0.002 TYR E 207 ARG 0.006 0.001 ARG D 214 *********************** 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 177 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6876 (p90) cc_final: 0.5986 (p90) REVERT: D 204 LEU cc_start: 0.6343 (tp) cc_final: 0.6017 (tt) REVERT: d 294 MET cc_start: -0.1512 (OUTLIER) cc_final: -0.1832 (mtp) REVERT: e 101 MET cc_start: 0.5510 (mmm) cc_final: 0.3680 (tpt) REVERT: a 4 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5190 (ttp80) REVERT: a 65 LYS cc_start: 0.2020 (OUTLIER) cc_final: 0.1582 (pttt) outliers start: 33 outliers final: 12 residues processed: 169 average time/residue: 0.2330 time to fit residues: 55.3282 Evaluate side-chains 145 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR 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 230 HIS Chi-restraints excluded: chain d residue 280 ASP 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 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 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- 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** ** 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 36 ASN ** e 92 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 = 0.5135 r_free = 0.5135 target = 0.193240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.144956 restraints weight = 77950.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.156837 restraints weight = 25119.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.160240 restraints weight = 13432.864| |-----------------------------------------------------------------------------| 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) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10765 Z= 0.223 Angle : 0.713 9.571 14545 Z= 0.370 Chirality : 0.046 0.250 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.852 25.764 1457 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.94 % Rotamer: Outliers : 2.92 % Allowed : 27.76 % 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: -1.25 (0.22), residues: 1325 helix: 0.24 (0.19), residues: 675 sheet: -0.45 (0.46), residues: 127 loop : -2.37 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP d 108 HIS 0.008 0.001 HIS A 36 PHE 0.020 0.002 PHE d 72 TYR 0.022 0.002 TYR A 24 ARG 0.006 0.001 ARG d 270 *********************** 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 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6696 (p90) cc_final: 0.5995 (p90) REVERT: D 204 LEU cc_start: 0.6337 (tp) cc_final: 0.6010 (tt) REVERT: E 132 HIS cc_start: 0.5213 (m-70) cc_final: 0.4660 (t-90) REVERT: d 1 MET cc_start: 0.3669 (pmm) cc_final: 0.2545 (ttt) REVERT: d 42 TYR cc_start: 0.6477 (p90) cc_final: 0.6271 (p90) REVERT: d 136 PHE cc_start: 0.2704 (OUTLIER) cc_final: 0.2167 (p90) REVERT: e 101 MET cc_start: 0.5589 (mmm) cc_final: 0.3468 (tpt) REVERT: A 16 LYS cc_start: 0.8599 (tppt) cc_final: 0.8385 (tppt) REVERT: a 4 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.4729 (ttp80) REVERT: a 65 LYS cc_start: 0.2129 (OUTLIER) cc_final: 0.1674 (pttt) outliers start: 33 outliers final: 18 residues processed: 156 average time/residue: 0.2248 time to fit residues: 49.6467 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 257 HIS Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE 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 67 LEU 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: 1.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 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 = 0.5151 r_free = 0.5151 target = 0.194418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.147637 restraints weight = 62856.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.158187 restraints weight = 20473.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.164652 restraints weight = 10441.672| |-----------------------------------------------------------------------------| r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4799 r_free = 0.4799 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4799 r_free = 0.4799 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10765 Z= 0.202 Angle : 0.690 8.594 14545 Z= 0.357 Chirality : 0.045 0.257 1619 Planarity : 0.004 0.103 1845 Dihedral : 5.678 24.499 1457 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % Rotamer: Outliers : 3.54 % Allowed : 26.79 % Favored : 69.67 % 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: 0.55 (0.20), residues: 657 sheet: -0.24 (0.48), residues: 126 loop : -2.26 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 108 HIS 0.007 0.001 HIS A 36 PHE 0.020 0.002 PHE d 72 TYR 0.021 0.002 TYR D 207 ARG 0.005 0.001 ARG d 270 *********************** 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 171 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6834 (p90) cc_final: 0.6103 (p90) REVERT: D 106 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7933 (ptt90) REVERT: D 204 LEU cc_start: 0.6057 (tp) cc_final: 0.5721 (tt) REVERT: E 132 HIS cc_start: 0.5112 (m-70) cc_final: 0.4622 (t-90) REVERT: d 1 MET cc_start: 0.4439 (pmm) cc_final: 0.3439 (ttt) REVERT: d 136 PHE cc_start: 0.2794 (OUTLIER) cc_final: 0.2280 (p90) REVERT: d 215 SER cc_start: 0.2352 (OUTLIER) cc_final: 0.1449 (t) REVERT: e 101 MET cc_start: 0.5479 (mmm) cc_final: 0.3611 (tpt) REVERT: a 65 LYS cc_start: 0.2673 (OUTLIER) cc_final: 0.2135 (pttt) outliers start: 40 outliers final: 19 residues processed: 162 average time/residue: 0.2267 time to fit residues: 52.3463 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 257 HIS 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 d residue 280 ASP 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 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 65 LYS 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: 20.0000 chunk 108 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.189873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142866 restraints weight = 59441.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.152210 restraints weight = 21573.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.156453 restraints weight = 11420.016| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 10765 Z= 0.283 Angle : 0.745 10.501 14545 Z= 0.387 Chirality : 0.047 0.291 1619 Planarity : 0.005 0.104 1845 Dihedral : 5.840 25.778 1457 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.21 % Favored : 93.56 % Rotamer: Outliers : 3.01 % Allowed : 26.97 % Favored : 70.03 % 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: -1.08 (0.23), residues: 1325 helix: 0.44 (0.19), residues: 670 sheet: -0.83 (0.45), residues: 145 loop : -2.26 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP d 108 HIS 0.018 0.002 HIS e 257 PHE 0.024 0.002 PHE d 72 TYR 0.025 0.002 TYR D 207 ARG 0.006 0.001 ARG E 96 *********************** 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 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6952 (p90) cc_final: 0.6700 (p90) REVERT: D 204 LEU cc_start: 0.5996 (tp) cc_final: 0.5721 (tt) REVERT: E 132 HIS cc_start: 0.5528 (m-70) cc_final: 0.4922 (t-90) REVERT: d 1 MET cc_start: 0.4192 (pmm) cc_final: 0.3311 (ttt) REVERT: d 136 PHE cc_start: 0.2915 (OUTLIER) cc_final: 0.1976 (p90) REVERT: d 215 SER cc_start: 0.2640 (OUTLIER) cc_final: 0.1987 (t) REVERT: d 263 MET cc_start: 0.6846 (pmm) cc_final: 0.6019 (pmm) REVERT: e 101 MET cc_start: 0.5829 (mmm) cc_final: 0.4012 (tpt) REVERT: e 178 LYS cc_start: 0.9143 (pttp) cc_final: 0.8513 (ptmm) REVERT: A 16 LYS cc_start: 0.8587 (tppt) cc_final: 0.8191 (tppt) REVERT: a 65 LYS cc_start: 0.2643 (OUTLIER) cc_final: 0.2121 (pttt) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 0.2167 time to fit residues: 47.8484 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 134 HIS 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 280 ASP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 132 HIS D 134 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 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 = 0.5158 r_free = 0.5158 target = 0.197888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.160173 restraints weight = 50066.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.169357 restraints weight = 21290.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.171903 restraints weight = 12284.974| |-----------------------------------------------------------------------------| r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.4559 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= 0.227 Angle : 0.720 10.118 14545 Z= 0.373 Chirality : 0.046 0.291 1619 Planarity : 0.004 0.103 1845 Dihedral : 5.646 24.325 1457 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.94 % Rotamer: Outliers : 2.65 % Allowed : 27.85 % 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: 0.53 (0.20), residues: 673 sheet: -0.75 (0.44), residues: 145 loop : -2.24 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 104 HIS 0.016 0.001 HIS e 257 PHE 0.023 0.002 PHE d 72 TYR 0.024 0.002 TYR d 177 ARG 0.010 0.001 ARG d 270 *********************** 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: 30 poor density : 127 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6933 (p90) cc_final: 0.6595 (p90) REVERT: D 204 LEU cc_start: 0.6234 (tp) cc_final: 0.5911 (tt) REVERT: E 132 HIS cc_start: 0.4874 (m-70) cc_final: 0.4494 (t-90) REVERT: E 224 ASN cc_start: 0.7029 (p0) cc_final: 0.6790 (m110) REVERT: d 1 MET cc_start: 0.4296 (pmm) cc_final: 0.3342 (ttt) REVERT: d 136 PHE cc_start: 0.3319 (OUTLIER) cc_final: 0.2127 (p90) REVERT: d 215 SER cc_start: 0.2522 (OUTLIER) cc_final: 0.1898 (t) REVERT: d 263 MET cc_start: 0.6621 (pmm) cc_final: 0.5786 (pmm) REVERT: e 101 MET cc_start: 0.5713 (mmm) cc_final: 0.3978 (tpt) REVERT: e 178 LYS cc_start: 0.8904 (pttp) cc_final: 0.8496 (pttm) REVERT: a 65 LYS cc_start: 0.2981 (OUTLIER) cc_final: 0.2408 (pttt) outliers start: 30 outliers final: 22 residues processed: 149 average time/residue: 0.2047 time to fit residues: 44.7389 Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 257 HIS 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 d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 113 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.201313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.167212 restraints weight = 80548.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.174394 restraints weight = 41437.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.180466 restraints weight = 16335.183| |-----------------------------------------------------------------------------| r_work (final): 0.4893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4892 r_free = 0.4892 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4892 r_free = 0.4892 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10765 Z= 0.187 Angle : 0.704 10.299 14545 Z= 0.361 Chirality : 0.045 0.285 1619 Planarity : 0.004 0.102 1845 Dihedral : 5.415 23.083 1457 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.30 % Favored : 94.47 % Rotamer: Outliers : 2.21 % Allowed : 28.21 % Favored : 69.58 % 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: -0.74 (0.23), residues: 1325 helix: 0.78 (0.20), residues: 661 sheet: -0.21 (0.49), residues: 125 loop : -2.24 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 104 HIS 0.016 0.001 HIS e 257 PHE 0.019 0.002 PHE d 72 TYR 0.019 0.001 TYR d 177 ARG 0.008 0.001 ARG d 270 *********************** 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: 25 poor density : 132 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6932 (p90) cc_final: 0.6332 (p90) REVERT: D 106 ARG cc_start: 0.8104 (ttm110) cc_final: 0.6445 (mmt180) REVERT: D 204 LEU cc_start: 0.6255 (tp) cc_final: 0.5899 (tt) REVERT: d 1 MET cc_start: 0.4851 (pmm) cc_final: 0.3899 (ttt) REVERT: d 136 PHE cc_start: 0.3628 (OUTLIER) cc_final: 0.2291 (p90) REVERT: d 263 MET cc_start: 0.6463 (pmm) cc_final: 0.5702 (pmm) REVERT: e 101 MET cc_start: 0.5566 (mmm) cc_final: 0.3973 (tpt) REVERT: e 178 LYS cc_start: 0.8661 (pttp) cc_final: 0.8262 (pttm) REVERT: A 16 LYS cc_start: 0.8439 (tppt) cc_final: 0.7761 (tppt) REVERT: a 65 LYS cc_start: 0.2662 (OUTLIER) cc_final: 0.2201 (pttt) outliers start: 25 outliers final: 18 residues processed: 152 average time/residue: 0.2066 time to fit residues: 45.8795 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 257 HIS 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 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 230 HIS 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 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 27 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.0020 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 132 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.195838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.157304 restraints weight = 56422.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.164610 restraints weight = 25211.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.169896 restraints weight = 14410.741| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4704 r_free = 0.4704 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 = 0.4704 r_free = 0.4704 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 10765 Z= 0.294 Angle : 0.765 10.644 14545 Z= 0.399 Chirality : 0.047 0.317 1619 Planarity : 0.005 0.102 1845 Dihedral : 5.641 26.055 1457 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 1.86 % Allowed : 27.76 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.96 (0.23), residues: 1325 helix: 0.63 (0.20), residues: 669 sheet: -0.87 (0.44), residues: 144 loop : -2.32 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 73 HIS 0.009 0.002 HIS A 36 PHE 0.026 0.002 PHE d 72 TYR 0.028 0.002 TYR D 207 ARG 0.009 0.001 ARG d 270 ********************** 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 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6841 (p90) cc_final: 0.6610 (p90) REVERT: D 106 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7686 (mtm110) REVERT: D 204 LEU cc_start: 0.6224 (tp) cc_final: 0.5899 (tt) REVERT: d 1 MET cc_start: 0.4661 (pmm) cc_final: 0.3863 (ttt) REVERT: d 136 PHE cc_start: 0.3729 (OUTLIER) cc_final: 0.2374 (p90) REVERT: d 263 MET cc_start: 0.6536 (pmm) cc_final: 0.5740 (pmm) REVERT: e 178 LYS cc_start: 0.8844 (pttp) cc_final: 0.8456 (pttm) REVERT: a 65 LYS cc_start: 0.3083 (OUTLIER) cc_final: 0.2500 (pttt) outliers start: 21 outliers final: 19 residues processed: 139 average time/residue: 0.2071 time to fit residues: 42.4327 Evaluate side-chains 138 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 257 HIS 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 d residue 280 ASP Chi-restraints excluded: chain e residue 13 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 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: 4.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 117 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 34 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.196773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.159526 restraints weight = 71000.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.168195 restraints weight = 34715.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.171157 restraints weight = 16260.448| |-----------------------------------------------------------------------------| r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10765 Z= 0.258 Angle : 0.754 10.481 14545 Z= 0.393 Chirality : 0.047 0.301 1619 Planarity : 0.004 0.100 1845 Dihedral : 5.625 25.063 1457 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.76 % Favored : 94.02 % Rotamer: Outliers : 2.12 % Allowed : 27.59 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.23), residues: 1325 helix: 0.56 (0.20), residues: 674 sheet: -0.91 (0.44), residues: 145 loop : -2.22 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP d 218 HIS 0.009 0.001 HIS A 36 PHE 0.027 0.002 PHE d 72 TYR 0.025 0.002 TYR D 207 ARG 0.010 0.001 ARG d 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4426.51 seconds wall clock time: 80 minutes 10.66 seconds (4810.66 seconds total)