Starting phenix.real_space_refine on Mon Apr 6 01:07:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y80_72676/04_2026/9y80_72676.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 90 5.16 5 C 9390 2.51 5 N 2296 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14393 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2794 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2794 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2794 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 67 Unusual residues: {'PX4': 3, 'RI5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PX4:plan-1': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'PX4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PX4:plan-1': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'PX4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PX4:plan-1': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'PX4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'NAG': 2, 'PX4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PX4:plan-1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.66, per 1000 atoms: 0.25 Number of scatterers: 14393 At special positions: 0 Unit cell: (93.24, 91.56, 130.2, 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 90 16.00 O 2617 8.00 N 2296 7.00 C 9390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 72 " " NAG A 502 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 502 " - " ASN E 72 " " NAG E 503 " - " ASN E 103 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 40.6% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.522A pdb=" N PHE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.603A pdb=" N SER A 56 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.629A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.812A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.523A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.568A pdb=" N ARG A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 410 through 443 removed outlier: 3.868A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 53 removed outlier: 4.226A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 57 removed outlier: 4.189A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.594A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.582A pdb=" N TYR B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.567A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 282 through 305 Processing helix chain 'B' and resid 315 through 344 Processing helix chain 'B' and resid 411 through 443 removed outlier: 3.869A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.975A pdb=" N LEU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 removed outlier: 4.172A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.633A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 removed outlier: 3.747A pdb=" N ILE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.619A pdb=" N ARG C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 removed outlier: 3.502A pdb=" N ARG C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 443 removed outlier: 3.851A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'D' and resid 43 through 53 removed outlier: 3.504A pdb=" N PHE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 57 removed outlier: 4.221A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.500A pdb=" N ALA D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.725A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 126 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.623A pdb=" N ILE D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 274 through 277 Processing helix chain 'D' and resid 282 through 305 removed outlier: 3.627A pdb=" N ARG D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 343 removed outlier: 3.539A pdb=" N ARG D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 443 removed outlier: 3.954A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'E' and resid 43 through 52 removed outlier: 3.566A pdb=" N PHE E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.581A pdb=" N SER E 56 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 57' Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.566A pdb=" N MET E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.856A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 260 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 282 through 305 removed outlier: 3.507A pdb=" N GLY E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 343 removed outlier: 3.761A pdb=" N TYR E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 443 removed outlier: 3.895A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing helix chain 'E' and resid 443 through 449 removed outlier: 3.694A pdb=" N GLU E 447 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP E 448 " --> pdb=" O ILE E 444 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 443 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.455A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 78 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 71 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 203 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 73 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.725A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ARG A 165 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 78 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 7.606A pdb=" N CYS A 243 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY A 230 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU A 245 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU A 228 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 247 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU A 226 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS A 249 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 236 removed outlier: 3.635A pdb=" N GLY A 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.383A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 78 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 71 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLU B 203 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 73 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.673A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE B 142 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG B 165 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 78 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AB1, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.411A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 137 through 142 removed outlier: 6.705A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE C 142 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ARG C 165 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 removed outlier: 3.639A pdb=" N GLU C 245 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 230 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 228 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB6, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.567A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 78 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.606A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE D 142 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ARG D 165 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 78 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 removed outlier: 3.623A pdb=" N GLU D 245 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 236 removed outlier: 3.502A pdb=" N LYS D 234 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.507A pdb=" N LEU E 152 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 78 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL E 71 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU E 203 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL E 73 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.703A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE E 142 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG E 165 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 78 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.581A pdb=" N GLU E 245 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY E 230 " --> pdb=" O GLU E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 234 through 236 removed outlier: 3.518A pdb=" N LYS E 234 " --> pdb=" O PHE E 241 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2355 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: 2.86 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2244 1.31 - 1.44: 4116 1.44 - 1.57: 8174 1.57 - 1.70: 47 1.70 - 1.84: 150 Bond restraints: 14731 Sorted by residual: bond pdb=" C23 PX4 B 506 " pdb=" O7 PX4 B 506 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C23 PX4 C 504 " pdb=" O7 PX4 C 504 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 PX4 A 506 " pdb=" O7 PX4 A 506 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 PX4 C 506 " pdb=" O7 PX4 C 506 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 PX4 D 507 " pdb=" O7 PX4 D 507 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 14726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 19340 2.26 - 4.52: 502 4.52 - 6.78: 56 6.78 - 9.03: 22 9.03 - 11.29: 2 Bond angle restraints: 19922 Sorted by residual: angle pdb=" O VAL D 210 " pdb=" C VAL D 210 " pdb=" N GLN D 211 " ideal model delta sigma weight residual 123.20 118.64 4.56 1.08e+00 8.57e-01 1.78e+01 angle pdb=" O LEU D 205 " pdb=" C LEU D 205 " pdb=" N SER D 206 " ideal model delta sigma weight residual 122.89 117.82 5.07 1.22e+00 6.72e-01 1.72e+01 angle pdb=" O VAL C 210 " pdb=" C VAL C 210 " pdb=" N GLN C 211 " ideal model delta sigma weight residual 123.20 118.74 4.46 1.08e+00 8.57e-01 1.70e+01 angle pdb=" CA VAL D 210 " pdb=" C VAL D 210 " pdb=" N GLN D 211 " ideal model delta sigma weight residual 116.40 120.91 -4.51 1.12e+00 7.97e-01 1.62e+01 angle pdb=" CA LEU D 205 " pdb=" C LEU D 205 " pdb=" N SER D 206 " ideal model delta sigma weight residual 115.88 121.02 -5.14 1.28e+00 6.10e-01 1.61e+01 ... (remaining 19917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 8121 17.27 - 34.53: 657 34.53 - 51.80: 153 51.80 - 69.07: 41 69.07 - 86.33: 14 Dihedral angle restraints: 8986 sinusoidal: 3883 harmonic: 5103 Sorted by residual: dihedral pdb=" CA ASP E 131 " pdb=" CB ASP E 131 " pdb=" CG ASP E 131 " pdb=" OD1 ASP E 131 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASP A 207 " pdb=" CB ASP A 207 " pdb=" CG ASP A 207 " pdb=" OD1 ASP A 207 " ideal model delta sinusoidal sigma weight residual -30.00 -83.32 53.32 1 2.00e+01 2.50e-03 9.66e+00 dihedral pdb=" CA ASP C 207 " pdb=" CB ASP C 207 " pdb=" CG ASP C 207 " pdb=" OD1 ASP C 207 " ideal model delta sinusoidal sigma weight residual -30.00 -83.31 53.31 1 2.00e+01 2.50e-03 9.66e+00 ... (remaining 8983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1944 0.064 - 0.128: 280 0.128 - 0.192: 22 0.192 - 0.256: 1 0.256 - 0.320: 1 Chirality restraints: 2248 Sorted by residual: chirality pdb=" C06 RI5 A 504 " pdb=" C05 RI5 A 504 " pdb=" C07 RI5 A 504 " pdb=" O19 RI5 A 504 " both_signs ideal model delta sigma weight residual False 2.58 2.90 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C08 RI5 A 504 " pdb=" C07 RI5 A 504 " pdb=" C09 RI5 A 504 " pdb=" C13 RI5 A 504 " both_signs ideal model delta sigma weight residual False 2.99 2.74 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PHE D 97 " pdb=" N PHE D 97 " pdb=" C PHE D 97 " pdb=" CB PHE D 97 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 2245 not shown) Planarity restraints: 2473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 99 " -0.242 9.50e-02 1.11e+02 1.09e-01 7.22e+00 pdb=" NE ARG A 99 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 99 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 99 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 99 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 145 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C VAL B 145 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 145 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 146 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 99 " 0.185 9.50e-02 1.11e+02 8.29e-02 4.22e+00 pdb=" NE ARG E 99 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 99 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 99 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 99 " 0.007 2.00e-02 2.50e+03 ... (remaining 2470 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3471 2.80 - 3.32: 13043 3.32 - 3.85: 22720 3.85 - 4.37: 27651 4.37 - 4.90: 48212 Nonbonded interactions: 115097 Sorted by model distance: nonbonded pdb=" OH TYR A 195 " pdb=" OD1 ASP E 120 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR E 196 " pdb=" OD1 ASN E 198 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR A 196 " pdb=" OD1 ASN A 198 " model vdw 2.285 3.040 nonbonded pdb=" OE1 GLN C 220 " pdb=" OH TYR C 257 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLN E 220 " pdb=" OH TYR E 257 " model vdw 2.313 3.040 ... (remaining 115092 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 42 through 409 or resid 411 through 449 or resid 503 or (r \ esid 506 and (name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C34 or na \ me O7 or name O8 )))) selection = (chain 'B' and (resid 42 through 449 or resid 503 or resid 506)) selection = (chain 'C' and (resid 42 through 409 or resid 411 through 449 or resid 503 or (r \ esid 506 and (name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C34 or na \ me O7 or name O8 )))) selection = (chain 'D' and (resid 42 through 449 or resid 503 or (resid 506 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name O7 or name O8 )))) selection = (chain 'E' and (resid 42 through 449 or resid 501 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name O7 or name O8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.680 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 14751 Z= 0.371 Angle : 0.821 11.293 19972 Z= 0.418 Chirality : 0.045 0.320 2248 Planarity : 0.004 0.109 2463 Dihedral : 13.804 86.335 5644 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1706 helix: -0.05 (0.20), residues: 595 sheet: 0.16 (0.29), residues: 336 loop : -0.45 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 61 TYR 0.011 0.001 TYR E 335 PHE 0.012 0.001 PHE B 134 TRP 0.006 0.001 TRP E 128 HIS 0.006 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00687 (14731) covalent geometry : angle 0.80783 (19922) SS BOND : bond 0.00135 ( 10) SS BOND : angle 2.88007 ( 20) hydrogen bonds : bond 0.27566 ( 682) hydrogen bonds : angle 8.71107 ( 2355) link_NAG-ASN : bond 0.00756 ( 10) link_NAG-ASN : angle 3.05353 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.547 Fit side-chains REVERT: B 46 ASP cc_start: 0.8358 (p0) cc_final: 0.8085 (p0) REVERT: B 49 ASP cc_start: 0.8003 (t0) cc_final: 0.7759 (t0) REVERT: B 144 ASP cc_start: 0.7566 (p0) cc_final: 0.7180 (p0) REVERT: B 260 GLN cc_start: 0.9079 (tp40) cc_final: 0.8647 (tp40) REVERT: C 144 ASP cc_start: 0.7825 (p0) cc_final: 0.6820 (t0) REVERT: D 144 ASP cc_start: 0.7390 (p0) cc_final: 0.6981 (p0) REVERT: D 428 LEU cc_start: 0.8867 (tp) cc_final: 0.8655 (mm) REVERT: E 261 MET cc_start: 0.8493 (mtt) cc_final: 0.8235 (mtt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0977 time to fit residues: 37.5462 Evaluate side-chains 182 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 344 GLN D 149 ASN D 446 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086501 restraints weight = 25569.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090013 restraints weight = 11939.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092377 restraints weight = 7412.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093908 restraints weight = 5404.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094790 restraints weight = 4358.907| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14751 Z= 0.131 Angle : 0.592 8.307 19972 Z= 0.304 Chirality : 0.043 0.191 2248 Planarity : 0.004 0.031 2463 Dihedral : 7.801 77.414 2318 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.29 % Allowed : 7.97 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1706 helix: 1.82 (0.21), residues: 582 sheet: 0.65 (0.29), residues: 350 loop : -0.25 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.031 0.001 TYR C 335 PHE 0.015 0.001 PHE D 433 TRP 0.010 0.001 TRP C 102 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00278 (14731) covalent geometry : angle 0.57923 (19922) SS BOND : bond 0.00488 ( 10) SS BOND : angle 1.41969 ( 20) hydrogen bonds : bond 0.05061 ( 682) hydrogen bonds : angle 5.31792 ( 2355) link_NAG-ASN : bond 0.00722 ( 10) link_NAG-ASN : angle 3.05171 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 46 ASP cc_start: 0.8358 (p0) cc_final: 0.8152 (p0) REVERT: B 49 ASP cc_start: 0.8191 (t0) cc_final: 0.7788 (t0) REVERT: B 417 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7973 (ttm110) REVERT: C 90 MET cc_start: 0.8716 (mtt) cc_final: 0.8514 (mtp) REVERT: C 144 ASP cc_start: 0.7812 (p0) cc_final: 0.7286 (p0) REVERT: D 137 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 144 ASP cc_start: 0.7427 (p0) cc_final: 0.6850 (p0) REVERT: D 261 MET cc_start: 0.7820 (mtt) cc_final: 0.7615 (mtt) REVERT: E 297 MET cc_start: 0.8956 (mmm) cc_final: 0.8541 (mmm) outliers start: 20 outliers final: 8 residues processed: 238 average time/residue: 0.0963 time to fit residues: 36.2180 Evaluate side-chains 195 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 198 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS A 450 HIS D 220 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084509 restraints weight = 25857.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087988 restraints weight = 11956.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090320 restraints weight = 7409.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091865 restraints weight = 5396.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092758 restraints weight = 4339.192| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14751 Z= 0.150 Angle : 0.575 10.055 19972 Z= 0.292 Chirality : 0.042 0.178 2248 Planarity : 0.003 0.030 2463 Dihedral : 7.332 73.925 2318 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.74 % Allowed : 9.90 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1706 helix: 2.10 (0.21), residues: 579 sheet: 0.92 (0.29), residues: 344 loop : -0.27 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.030 0.002 TYR C 335 PHE 0.012 0.001 PHE D 433 TRP 0.009 0.001 TRP A 102 HIS 0.012 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00348 (14731) covalent geometry : angle 0.56524 (19922) SS BOND : bond 0.00447 ( 10) SS BOND : angle 1.08735 ( 20) hydrogen bonds : bond 0.04514 ( 682) hydrogen bonds : angle 4.99361 ( 2355) link_NAG-ASN : bond 0.00547 ( 10) link_NAG-ASN : angle 2.60850 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8071 (p0) cc_final: 0.7836 (p0) REVERT: A 207 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7221 (p0) REVERT: A 428 LEU cc_start: 0.9311 (tt) cc_final: 0.9077 (mp) REVERT: B 49 ASP cc_start: 0.8177 (t0) cc_final: 0.7747 (t0) REVERT: B 417 ARG cc_start: 0.8237 (tpp80) cc_final: 0.8035 (ttm110) REVERT: C 90 MET cc_start: 0.8769 (mtt) cc_final: 0.8418 (mtp) REVERT: C 144 ASP cc_start: 0.7818 (p0) cc_final: 0.7438 (p0) REVERT: D 50 LYS cc_start: 0.8851 (tmmt) cc_final: 0.8633 (pptt) REVERT: D 144 ASP cc_start: 0.7545 (p0) cc_final: 0.6966 (p0) outliers start: 27 outliers final: 15 residues processed: 207 average time/residue: 0.0950 time to fit residues: 31.2838 Evaluate side-chains 191 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 198 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.0070 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS B 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085410 restraints weight = 25906.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088822 restraints weight = 11943.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091139 restraints weight = 7419.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092646 restraints weight = 5399.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.093539 restraints weight = 4345.901| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14751 Z= 0.121 Angle : 0.538 7.912 19972 Z= 0.275 Chirality : 0.042 0.180 2248 Planarity : 0.003 0.031 2463 Dihedral : 6.779 66.847 2318 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.99 % Allowed : 11.38 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1706 helix: 2.09 (0.21), residues: 596 sheet: 1.07 (0.29), residues: 344 loop : -0.16 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.028 0.001 TYR C 335 PHE 0.013 0.001 PHE C 433 TRP 0.008 0.001 TRP C 102 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00276 (14731) covalent geometry : angle 0.52840 (19922) SS BOND : bond 0.00252 ( 10) SS BOND : angle 1.54453 ( 20) hydrogen bonds : bond 0.03853 ( 682) hydrogen bonds : angle 4.70358 ( 2355) link_NAG-ASN : bond 0.00571 ( 10) link_NAG-ASN : angle 2.35374 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.7326 (ttp) cc_final: 0.7082 (ttp) REVERT: A 258 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 334 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8630 (tm-30) REVERT: B 49 ASP cc_start: 0.8163 (t0) cc_final: 0.7662 (t0) REVERT: B 300 GLN cc_start: 0.9055 (mt0) cc_final: 0.8827 (mt0) REVERT: C 90 MET cc_start: 0.8724 (mtt) cc_final: 0.8350 (mtp) REVERT: C 137 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 144 ASP cc_start: 0.7741 (p0) cc_final: 0.7467 (p0) REVERT: D 50 LYS cc_start: 0.8862 (tmmt) cc_final: 0.8625 (pptt) REVERT: D 144 ASP cc_start: 0.7497 (p0) cc_final: 0.6885 (p0) REVERT: D 261 MET cc_start: 0.7860 (mtt) cc_final: 0.7607 (mtt) REVERT: E 137 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8127 (tm-30) outliers start: 31 outliers final: 12 residues processed: 203 average time/residue: 0.0995 time to fit residues: 31.6228 Evaluate side-chains 193 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 144 optimal weight: 0.0470 chunk 94 optimal weight: 3.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS B 100 GLN B 235 HIS B 344 GLN C 141 ASN C 235 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083955 restraints weight = 25981.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087409 restraints weight = 11969.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089712 restraints weight = 7414.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.091222 restraints weight = 5398.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092117 restraints weight = 4346.255| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14751 Z= 0.148 Angle : 0.547 9.640 19972 Z= 0.280 Chirality : 0.042 0.259 2248 Planarity : 0.003 0.031 2463 Dihedral : 6.443 59.254 2318 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.93 % Allowed : 12.08 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1706 helix: 2.25 (0.21), residues: 578 sheet: 1.05 (0.29), residues: 344 loop : -0.22 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 305 TYR 0.027 0.002 TYR C 335 PHE 0.011 0.001 PHE B 133 TRP 0.008 0.001 TRP A 102 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00345 (14731) covalent geometry : angle 0.53853 (19922) SS BOND : bond 0.00360 ( 10) SS BOND : angle 1.31128 ( 20) hydrogen bonds : bond 0.03826 ( 682) hydrogen bonds : angle 4.69217 ( 2355) link_NAG-ASN : bond 0.00480 ( 10) link_NAG-ASN : angle 2.27391 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8754 (tm-30) REVERT: B 49 ASP cc_start: 0.8198 (t0) cc_final: 0.7736 (t0) REVERT: B 417 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7890 (ttp-110) REVERT: C 90 MET cc_start: 0.8780 (mtt) cc_final: 0.8418 (mtp) REVERT: C 144 ASP cc_start: 0.7687 (p0) cc_final: 0.7436 (p0) REVERT: D 50 LYS cc_start: 0.8861 (tmmt) cc_final: 0.8621 (pptt) REVERT: D 144 ASP cc_start: 0.7484 (p0) cc_final: 0.6821 (p0) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.0963 time to fit residues: 30.0529 Evaluate side-chains 194 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 160 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083209 restraints weight = 26034.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086573 restraints weight = 12111.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088829 restraints weight = 7579.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090204 restraints weight = 5557.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091225 restraints weight = 4544.874| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14751 Z= 0.162 Angle : 0.558 9.328 19972 Z= 0.286 Chirality : 0.043 0.261 2248 Planarity : 0.003 0.032 2463 Dihedral : 6.253 52.741 2318 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.19 % Allowed : 12.47 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1706 helix: 2.27 (0.21), residues: 578 sheet: 0.98 (0.29), residues: 347 loop : -0.23 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 305 TYR 0.027 0.002 TYR C 335 PHE 0.012 0.001 PHE B 133 TRP 0.008 0.001 TRP A 102 HIS 0.002 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00379 (14731) covalent geometry : angle 0.55019 (19922) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.23469 ( 20) hydrogen bonds : bond 0.03790 ( 682) hydrogen bonds : angle 4.66988 ( 2355) link_NAG-ASN : bond 0.00486 ( 10) link_NAG-ASN : angle 2.28691 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8685 (tm-30) REVERT: B 49 ASP cc_start: 0.8180 (t0) cc_final: 0.7692 (t0) REVERT: B 305 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8156 (mtm-85) REVERT: B 417 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7886 (ttp-110) REVERT: C 90 MET cc_start: 0.8765 (mtt) cc_final: 0.8434 (mtp) REVERT: C 144 ASP cc_start: 0.7641 (p0) cc_final: 0.7412 (p0) REVERT: D 50 LYS cc_start: 0.8883 (tmmt) cc_final: 0.8634 (pptt) REVERT: D 144 ASP cc_start: 0.7521 (p0) cc_final: 0.6900 (p0) outliers start: 34 outliers final: 23 residues processed: 194 average time/residue: 0.0872 time to fit residues: 27.4267 Evaluate side-chains 194 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083182 restraints weight = 25946.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.086573 restraints weight = 11957.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088867 restraints weight = 7434.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090211 restraints weight = 5420.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091315 restraints weight = 4431.140| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14751 Z= 0.154 Angle : 0.568 11.546 19972 Z= 0.288 Chirality : 0.043 0.251 2248 Planarity : 0.003 0.032 2463 Dihedral : 6.127 49.299 2318 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.19 % Allowed : 12.79 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1706 helix: 2.29 (0.21), residues: 578 sheet: 1.01 (0.29), residues: 344 loop : -0.21 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.027 0.002 TYR C 335 PHE 0.012 0.001 PHE B 133 TRP 0.008 0.001 TRP A 102 HIS 0.002 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00366 (14731) covalent geometry : angle 0.56061 (19922) SS BOND : bond 0.00352 ( 10) SS BOND : angle 1.15810 ( 20) hydrogen bonds : bond 0.03771 ( 682) hydrogen bonds : angle 4.65583 ( 2355) link_NAG-ASN : bond 0.00491 ( 10) link_NAG-ASN : angle 2.24334 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8703 (tm-30) REVERT: B 49 ASP cc_start: 0.8193 (t0) cc_final: 0.7847 (t0) REVERT: B 55 THR cc_start: 0.8886 (p) cc_final: 0.8381 (p) REVERT: B 300 GLN cc_start: 0.9029 (mt0) cc_final: 0.8792 (mt0) REVERT: B 417 ARG cc_start: 0.8405 (ttm110) cc_final: 0.7888 (ttp-110) REVERT: C 90 MET cc_start: 0.8802 (mtt) cc_final: 0.8455 (mtp) REVERT: C 144 ASP cc_start: 0.7628 (p0) cc_final: 0.7420 (p0) REVERT: D 50 LYS cc_start: 0.8861 (tmmt) cc_final: 0.8599 (pptt) REVERT: D 144 ASP cc_start: 0.7542 (p0) cc_final: 0.6920 (p0) outliers start: 34 outliers final: 31 residues processed: 193 average time/residue: 0.0924 time to fit residues: 28.7368 Evaluate side-chains 206 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 138 optimal weight: 0.0020 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083980 restraints weight = 25856.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087425 restraints weight = 11928.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.089717 restraints weight = 7368.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091072 restraints weight = 5370.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092185 restraints weight = 4375.812| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14751 Z= 0.139 Angle : 0.570 10.550 19972 Z= 0.289 Chirality : 0.042 0.250 2248 Planarity : 0.003 0.033 2463 Dihedral : 6.022 52.423 2318 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.99 % Allowed : 13.11 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1706 helix: 2.21 (0.21), residues: 589 sheet: 0.87 (0.28), residues: 386 loop : -0.06 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.027 0.001 TYR C 335 PHE 0.012 0.001 PHE B 133 TRP 0.007 0.001 TRP E 102 HIS 0.002 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00334 (14731) covalent geometry : angle 0.55907 (19922) SS BOND : bond 0.00348 ( 10) SS BOND : angle 2.34472 ( 20) hydrogen bonds : bond 0.03678 ( 682) hydrogen bonds : angle 4.59320 ( 2355) link_NAG-ASN : bond 0.00502 ( 10) link_NAG-ASN : angle 2.17690 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8646 (tm-30) REVERT: B 49 ASP cc_start: 0.8187 (t0) cc_final: 0.7843 (t0) REVERT: B 55 THR cc_start: 0.8891 (p) cc_final: 0.8380 (p) REVERT: B 300 GLN cc_start: 0.9027 (mt0) cc_final: 0.8783 (mt0) REVERT: B 417 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7880 (ttp-110) REVERT: C 90 MET cc_start: 0.8784 (mtt) cc_final: 0.8437 (mtp) REVERT: D 50 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8594 (pptt) REVERT: D 144 ASP cc_start: 0.7517 (p0) cc_final: 0.6893 (p0) outliers start: 31 outliers final: 25 residues processed: 193 average time/residue: 0.0897 time to fit residues: 28.3508 Evaluate side-chains 197 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085899 restraints weight = 25790.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089395 restraints weight = 11862.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091736 restraints weight = 7295.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093252 restraints weight = 5274.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094161 restraints weight = 4224.138| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14751 Z= 0.106 Angle : 0.556 11.483 19972 Z= 0.280 Chirality : 0.042 0.243 2248 Planarity : 0.003 0.034 2463 Dihedral : 5.708 57.847 2318 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 13.82 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1706 helix: 2.40 (0.21), residues: 569 sheet: 0.98 (0.28), residues: 374 loop : -0.14 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 305 TYR 0.026 0.001 TYR C 335 PHE 0.012 0.001 PHE C 433 TRP 0.008 0.001 TRP E 102 HIS 0.003 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00250 (14731) covalent geometry : angle 0.54665 (19922) SS BOND : bond 0.00301 ( 10) SS BOND : angle 2.17853 ( 20) hydrogen bonds : bond 0.03432 ( 682) hydrogen bonds : angle 4.42583 ( 2355) link_NAG-ASN : bond 0.00537 ( 10) link_NAG-ASN : angle 1.98066 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8852 (mp10) REVERT: A 334 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 445 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7678 (mtt180) REVERT: B 49 ASP cc_start: 0.8193 (t0) cc_final: 0.7839 (t0) REVERT: B 55 THR cc_start: 0.8894 (p) cc_final: 0.8377 (p) REVERT: B 232 CYS cc_start: 0.5849 (t) cc_final: 0.5334 (t) REVERT: B 300 GLN cc_start: 0.8979 (mt0) cc_final: 0.8739 (mt0) REVERT: B 305 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8218 (mtm-85) REVERT: B 417 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7865 (ttp-110) REVERT: C 90 MET cc_start: 0.8729 (mtt) cc_final: 0.8374 (mtp) REVERT: D 50 LYS cc_start: 0.8801 (tmmt) cc_final: 0.8565 (pptt) REVERT: D 144 ASP cc_start: 0.7421 (p0) cc_final: 0.6801 (p0) REVERT: E 89 THR cc_start: 0.9067 (p) cc_final: 0.8775 (t) outliers start: 25 outliers final: 19 residues processed: 203 average time/residue: 0.0910 time to fit residues: 29.7541 Evaluate side-chains 199 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084353 restraints weight = 25931.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087795 restraints weight = 11976.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090080 restraints weight = 7406.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091586 restraints weight = 5395.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092482 restraints weight = 4346.140| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14751 Z= 0.151 Angle : 0.589 12.306 19972 Z= 0.296 Chirality : 0.043 0.243 2248 Planarity : 0.003 0.033 2463 Dihedral : 5.789 57.199 2318 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 14.85 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1706 helix: 2.48 (0.21), residues: 554 sheet: 0.92 (0.28), residues: 374 loop : -0.22 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.027 0.001 TYR C 335 PHE 0.012 0.001 PHE B 133 TRP 0.008 0.001 TRP A 102 HIS 0.004 0.000 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00363 (14731) covalent geometry : angle 0.57925 (19922) SS BOND : bond 0.00368 ( 10) SS BOND : angle 2.29129 ( 20) hydrogen bonds : bond 0.03613 ( 682) hydrogen bonds : angle 4.56995 ( 2355) link_NAG-ASN : bond 0.00454 ( 10) link_NAG-ASN : angle 2.09973 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 445 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7638 (mtt180) REVERT: B 49 ASP cc_start: 0.8201 (t0) cc_final: 0.7862 (t0) REVERT: B 55 THR cc_start: 0.8913 (p) cc_final: 0.8402 (p) REVERT: B 232 CYS cc_start: 0.5802 (t) cc_final: 0.5362 (t) REVERT: B 300 GLN cc_start: 0.8994 (mt0) cc_final: 0.8763 (mt0) REVERT: B 417 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7869 (ttp-110) REVERT: C 90 MET cc_start: 0.8766 (mtt) cc_final: 0.8420 (mtp) REVERT: D 50 LYS cc_start: 0.8852 (tmmt) cc_final: 0.8610 (pptt) outliers start: 21 outliers final: 19 residues processed: 189 average time/residue: 0.1025 time to fit residues: 30.7452 Evaluate side-chains 190 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 0.0370 chunk 104 optimal weight: 0.0470 chunk 77 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084797 restraints weight = 25929.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088254 restraints weight = 11974.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.090580 restraints weight = 7392.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.091960 restraints weight = 5361.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093064 restraints weight = 4361.055| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14751 Z= 0.129 Angle : 0.591 12.322 19972 Z= 0.293 Chirality : 0.043 0.230 2248 Planarity : 0.003 0.034 2463 Dihedral : 5.686 50.732 2318 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.29 % Allowed : 15.30 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1706 helix: 2.30 (0.21), residues: 569 sheet: 0.94 (0.28), residues: 373 loop : -0.16 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 305 TYR 0.026 0.001 TYR C 335 PHE 0.012 0.001 PHE B 133 TRP 0.015 0.001 TRP A 438 HIS 0.003 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00310 (14731) covalent geometry : angle 0.58130 (19922) SS BOND : bond 0.00301 ( 10) SS BOND : angle 2.44694 ( 20) hydrogen bonds : bond 0.03506 ( 682) hydrogen bonds : angle 4.53394 ( 2355) link_NAG-ASN : bond 0.00495 ( 10) link_NAG-ASN : angle 2.04671 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.82 seconds wall clock time: 32 minutes 58.83 seconds (1978.83 seconds total)