Starting phenix.real_space_refine on Sat Sep 12 05:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jaf_6346/09_2026/3jaf_6346.map" } resolution = 3.8 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= 1.000 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 9115 2.51 5 N 2210 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13865 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2683 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 325} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.24 Number of scatterers: 13865 At special positions: 0 Unit cell: (95.68, 97.76, 127.92, 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 2450 8.00 N 2210 7.00 C 9115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 571.9 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.6% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.745A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 Processing helix chain 'B' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.745A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.535A pdb=" N TYR C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 Processing helix chain 'C' and resid 328 through 363 removed outlier: 3.600A pdb=" N THR C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.746A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 361 " --> pdb=" O TYR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.277A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.745A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 361 " --> pdb=" O TYR D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 235 through 243 removed outlier: 4.534A pdb=" N TYR E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 260 removed outlier: 3.979A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 254 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 290 removed outlier: 3.899A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 290 " --> pdb=" O SER E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 Processing helix chain 'E' and resid 328 through 363 removed outlier: 3.599A pdb=" N THR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.745A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=D, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=E, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.842A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=H, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=I, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=L, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=M, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.922A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=P, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=Q, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.843A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.923A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=T, first strand: chain 'E' and resid 115 through 116 836 hydrogen bonds defined for protein. 2418 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: 2.62 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4069 1.34 - 1.46: 2905 1.46 - 1.58: 7121 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14245 Sorted by residual: bond pdb=" C46 IVM E 401 " pdb=" O12 IVM E 401 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C46 IVM A 503 " pdb=" O12 IVM A 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C46 IVM B 503 " pdb=" O12 IVM B 503 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C46 IVM D 503 " pdb=" O12 IVM D 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C46 IVM C 503 " pdb=" O12 IVM C 503 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17654 2.12 - 4.24: 1504 4.24 - 6.36: 228 6.36 - 8.48: 54 8.48 - 10.60: 5 Bond angle restraints: 19445 Sorted by residual: angle pdb=" N GLY B 327 " pdb=" CA GLY B 327 " pdb=" C GLY B 327 " ideal model delta sigma weight residual 111.42 122.02 -10.60 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY C 327 " pdb=" CA GLY C 327 " pdb=" C GLY C 327 " ideal model delta sigma weight residual 111.42 122.01 -10.59 1.51e+00 4.39e-01 4.92e+01 angle pdb=" N GLY D 327 " pdb=" CA GLY D 327 " pdb=" C GLY D 327 " ideal model delta sigma weight residual 111.42 122.00 -10.58 1.51e+00 4.39e-01 4.91e+01 angle pdb=" N GLY E 327 " pdb=" CA GLY E 327 " pdb=" C GLY E 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 111.42 121.99 -10.57 1.51e+00 4.39e-01 4.90e+01 ... (remaining 19440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 8415 24.30 - 48.59: 220 48.59 - 72.89: 55 72.89 - 97.19: 40 97.19 - 121.48: 85 Dihedral angle restraints: 8815 sinusoidal: 3765 harmonic: 5050 Sorted by residual: dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.47 78.47 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 8812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2029 0.080 - 0.159: 250 0.159 - 0.239: 11 0.239 - 0.319: 5 0.319 - 0.399: 5 Chirality restraints: 2300 Sorted by residual: chirality pdb=" C47 IVM D 503 " pdb=" C39 IVM D 503 " pdb=" C41 IVM D 503 " pdb=" C45 IVM D 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C47 IVM C 503 " pdb=" C39 IVM C 503 " pdb=" C41 IVM C 503 " pdb=" C45 IVM C 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C47 IVM B 503 " pdb=" C39 IVM B 503 " pdb=" C41 IVM B 503 " pdb=" C45 IVM B 503 " both_signs ideal model delta sigma weight residual False 3.13 2.73 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 2297 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 265 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 265 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO B 266 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 265 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 266 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 266 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 266 " -0.029 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 322 2.69 - 3.24: 14524 3.24 - 3.79: 20992 3.79 - 4.35: 28592 4.35 - 4.90: 45301 Nonbonded interactions: 109731 Sorted by model distance: nonbonded pdb=" O SER E 254 " pdb=" OG SER E 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER D 254 " pdb=" OG SER D 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER B 254 " pdb=" OG SER B 257 " model vdw 2.134 3.040 nonbonded pdb=" O SER C 254 " pdb=" OG SER C 257 " model vdw 2.135 3.040 ... (remaining 109726 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.140 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 14255 Z= 0.397 Angle : 1.344 10.595 19470 Z= 0.854 Chirality : 0.056 0.399 2300 Planarity : 0.005 0.054 2360 Dihedral : 18.872 121.482 5530 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.70 % Allowed : 1.06 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.18), residues: 1700 helix: -0.70 (0.20), residues: 540 sheet: 0.76 (0.25), residues: 340 loop : -0.92 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG C 229 TYR 0.026 0.003 TYR E 94 PHE 0.029 0.004 PHE E 29 TRP 0.023 0.003 TRP D 259 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.40 (14245) covalent geometry : angle 1.34460 / 0.85 (19445) SS BOND : bond 0.00709 / 0.39 ( 5) SS BOND : angle 0.46132 / 0.26 ( 10) hydrogen bonds : bond 0.14404 / 9.83 ( 691) hydrogen bonds : angle 9.58881 / 6.59 ( 2418) link_BETA1-4 : bond 0.01909 / 1.05 ( 5) link_BETA1-4 : angle 0.65823 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6955 (m-30) cc_final: 0.6657 (m-30) REVERT: D 100 ASP cc_start: 0.6599 (m-30) cc_final: 0.6179 (m-30) REVERT: D 130 ASP cc_start: 0.6910 (t0) cc_final: 0.6701 (t0) REVERT: E 89 LEU cc_start: 0.8164 (mt) cc_final: 0.7915 (mt) REVERT: E 100 ASP cc_start: 0.7263 (m-30) cc_final: 0.6800 (m-30) REVERT: E 271 LEU cc_start: 0.8884 (mt) cc_final: 0.8672 (mt) outliers start: 10 outliers final: 0 residues processed: 317 average time/residue: 0.1040 time to fit residues: 51.2813 Evaluate side-chains 176 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 131 ASN A 139 ASN A 354 ASN B 54 ASN B 131 ASN B 139 ASN B 354 ASN C 54 ASN C 235 GLN C 354 ASN D 54 ASN D 131 ASN D 354 ASN E 54 ASN E 131 ASN E 354 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.031789 restraints weight = 94515.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.032899 restraints weight = 54666.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033729 restraints weight = 36751.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.034308 restraints weight = 27126.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.034742 restraints weight = 21439.263| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14255 Z= 0.189 Angle : 0.877 9.212 19470 Z= 0.423 Chirality : 0.051 0.371 2300 Planarity : 0.006 0.050 2360 Dihedral : 13.239 86.980 2535 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.54 % Allowed : 8.73 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.19), residues: 1700 helix: 0.63 (0.20), residues: 575 sheet: 0.82 (0.25), residues: 380 loop : -0.52 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 212 TYR 0.020 0.002 TYR C 144 PHE 0.027 0.002 PHE D 353 TRP 0.007 0.001 TRP E 302 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (14245) covalent geometry : angle 0.87789 / 0.42 (19445) SS BOND : bond 0.00097 / 0.05 ( 5) SS BOND : angle 0.24946 / 0.14 ( 10) hydrogen bonds : bond 0.04886 / 3.22 ( 691) hydrogen bonds : angle 6.19021 / 4.23 ( 2418) link_BETA1-4 : bond 0.00892 / 0.40 ( 5) link_BETA1-4 : angle 0.42377 / 0.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8850 (ttp80) REVERT: A 94 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: A 152 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 156 MET cc_start: 0.8530 (ptp) cc_final: 0.8263 (mtp) REVERT: B 105 MET cc_start: 0.8901 (mmt) cc_final: 0.8525 (mmt) REVERT: C 72 MET cc_start: 0.8989 (tpt) cc_final: 0.8486 (tpp) REVERT: C 94 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: C 163 MET cc_start: 0.8853 (pmm) cc_final: 0.8627 (pmm) REVERT: C 240 LEU cc_start: 0.9377 (mp) cc_final: 0.9136 (pp) REVERT: C 251 VAL cc_start: 0.9628 (t) cc_final: 0.9125 (t) REVERT: C 252 ILE cc_start: 0.9678 (mt) cc_final: 0.9301 (mt) REVERT: C 255 TRP cc_start: 0.8989 (m-10) cc_final: 0.8441 (m-10) REVERT: C 282 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8914 (mm-40) REVERT: D 72 MET cc_start: 0.8777 (tpt) cc_final: 0.8566 (tpt) REVERT: D 101 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8777 (tp) REVERT: D 105 MET cc_start: 0.8905 (mmm) cc_final: 0.8387 (mmm) REVERT: D 152 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8897 (mm) REVERT: D 278 THR cc_start: 0.9255 (p) cc_final: 0.8893 (t) REVERT: D 279 MET cc_start: 0.9288 (tpp) cc_final: 0.9077 (tpp) REVERT: D 282 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8761 (mm-40) REVERT: D 303 MET cc_start: 0.9407 (mmm) cc_final: 0.9119 (mmm) REVERT: E 89 LEU cc_start: 0.9315 (mt) cc_final: 0.8963 (mt) REVERT: E 133 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8734 (pp) REVERT: E 152 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8619 (mm) REVERT: E 163 MET cc_start: 0.8907 (pmm) cc_final: 0.8690 (pmm) REVERT: E 179 MET cc_start: 0.8860 (tpp) cc_final: 0.8424 (mmm) REVERT: E 278 THR cc_start: 0.9212 (p) cc_final: 0.8875 (t) outliers start: 36 outliers final: 8 residues processed: 226 average time/residue: 0.0922 time to fit residues: 33.9627 Evaluate side-chains 174 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 166 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 231 HIS B 261 ASN C 131 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 166 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.038545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.030656 restraints weight = 97747.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.031762 restraints weight = 56183.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032601 restraints weight = 37348.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.033180 restraints weight = 27684.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.033618 restraints weight = 21829.067| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14255 Z= 0.249 Angle : 0.814 10.937 19470 Z= 0.403 Chirality : 0.045 0.207 2300 Planarity : 0.005 0.052 2360 Dihedral : 10.504 71.851 2535 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.10 % Allowed : 13.03 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.52 (0.20), residues: 1700 helix: 1.21 (0.21), residues: 575 sheet: 0.58 (0.25), residues: 385 loop : -0.40 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.024 0.002 TYR B 361 PHE 0.020 0.002 PHE E 353 TRP 0.007 0.001 TRP B 358 HIS 0.006 0.002 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (14245) covalent geometry : angle 0.81267 / 0.40 (19445) SS BOND : bond 0.00094 / 0.06 ( 5) SS BOND : angle 0.50486 / 0.31 ( 10) hydrogen bonds : bond 0.04577 / 2.98 ( 691) hydrogen bonds : angle 5.66171 / 3.87 ( 2418) link_BETA1-4 : bond 0.00845 / 0.39 ( 5) link_BETA1-4 : angle 1.64364 / 1.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8064 (tpp) cc_final: 0.7660 (tpp) REVERT: A 75 ARG cc_start: 0.9118 (ttm110) cc_final: 0.8896 (ttp80) REVERT: A 82 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8530 (mp10) REVERT: A 101 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 105 MET cc_start: 0.9009 (mmm) cc_final: 0.8308 (mmm) REVERT: A 152 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 156 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: A 282 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8912 (mm-40) REVERT: A 346 PHE cc_start: 0.8738 (m-80) cc_final: 0.8367 (m-80) REVERT: B 72 MET cc_start: 0.9039 (tpp) cc_final: 0.8777 (tpp) REVERT: B 82 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: B 101 LEU cc_start: 0.8680 (tp) cc_final: 0.8397 (tp) REVERT: B 179 MET cc_start: 0.9067 (tpp) cc_final: 0.8487 (mmm) REVERT: B 244 TYR cc_start: 0.9122 (m-80) cc_final: 0.8779 (m-80) REVERT: C 72 MET cc_start: 0.9067 (tpt) cc_final: 0.8703 (tpt) REVERT: C 101 LEU cc_start: 0.8785 (tp) cc_final: 0.8541 (tp) REVERT: C 179 MET cc_start: 0.8981 (tpp) cc_final: 0.8388 (mmm) REVERT: C 282 GLN cc_start: 0.9338 (mm-40) cc_final: 0.9021 (mm-40) REVERT: D 72 MET cc_start: 0.8880 (tpt) cc_final: 0.8638 (tpt) REVERT: D 152 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8829 (mm) REVERT: D 185 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8361 (mp0) REVERT: E 101 LEU cc_start: 0.8932 (tp) cc_final: 0.8685 (tp) REVERT: E 152 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8782 (mm) REVERT: E 163 MET cc_start: 0.8770 (pmm) cc_final: 0.8482 (pmm) REVERT: E 179 MET cc_start: 0.8830 (tpp) cc_final: 0.8477 (mmm) REVERT: E 249 LEU cc_start: 0.9335 (mt) cc_final: 0.9129 (mt) REVERT: E 278 THR cc_start: 0.9255 (p) cc_final: 0.8996 (t) outliers start: 44 outliers final: 18 residues processed: 191 average time/residue: 0.0954 time to fit residues: 29.5322 Evaluate side-chains 165 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 0.0020 overall best weight: 1.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.031823 restraints weight = 94918.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.032988 restraints weight = 54180.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033852 restraints weight = 35978.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.034445 restraints weight = 26722.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.034874 restraints weight = 21260.448| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14255 Z= 0.139 Angle : 0.752 12.040 19470 Z= 0.364 Chirality : 0.044 0.200 2300 Planarity : 0.004 0.041 2360 Dihedral : 8.047 67.553 2535 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.18 % Allowed : 15.35 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.54 (0.20), residues: 1700 helix: 1.39 (0.22), residues: 570 sheet: 0.58 (0.26), residues: 390 loop : -0.54 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.022 0.002 TYR C 144 PHE 0.021 0.001 PHE D 353 TRP 0.005 0.001 TRP B 302 HIS 0.001 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14245) covalent geometry : angle 0.75240 / 0.36 (19445) SS BOND : bond 0.00091 / 0.05 ( 5) SS BOND : angle 0.42467 / 0.28 ( 10) hydrogen bonds : bond 0.04065 / 2.66 ( 691) hydrogen bonds : angle 5.14273 / 3.51 ( 2418) link_BETA1-4 : bond 0.00565 / 0.32 ( 5) link_BETA1-4 : angle 0.96320 / 0.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8115 (tpp) cc_final: 0.7637 (tpp) REVERT: A 82 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8586 (mp10) REVERT: A 101 LEU cc_start: 0.9025 (tp) cc_final: 0.8734 (tp) REVERT: A 105 MET cc_start: 0.8961 (mmm) cc_final: 0.8292 (mmm) REVERT: A 152 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 156 MET cc_start: 0.8597 (ptp) cc_final: 0.8313 (mtp) REVERT: A 282 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8956 (mm-40) REVERT: A 300 ASP cc_start: 0.9135 (m-30) cc_final: 0.8895 (m-30) REVERT: B 72 MET cc_start: 0.9090 (tpp) cc_final: 0.8876 (tpp) REVERT: B 75 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8797 (ttp80) REVERT: B 101 LEU cc_start: 0.8711 (tp) cc_final: 0.8419 (tp) REVERT: B 179 MET cc_start: 0.9035 (tpp) cc_final: 0.8511 (mmm) REVERT: B 244 TYR cc_start: 0.9090 (m-80) cc_final: 0.8771 (m-80) REVERT: C 72 MET cc_start: 0.9122 (tpt) cc_final: 0.8729 (tpt) REVERT: C 75 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8842 (ttp80) REVERT: C 101 LEU cc_start: 0.8824 (tp) cc_final: 0.8554 (tp) REVERT: C 179 MET cc_start: 0.8901 (tpp) cc_final: 0.8413 (mmm) REVERT: C 243 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8704 (mpp) REVERT: C 282 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9014 (mm-40) REVERT: D 34 MET cc_start: 0.8295 (tpp) cc_final: 0.8028 (tpp) REVERT: D 72 MET cc_start: 0.9036 (tpt) cc_final: 0.8733 (tpt) REVERT: D 101 LEU cc_start: 0.8955 (tp) cc_final: 0.8709 (tp) REVERT: D 105 MET cc_start: 0.8898 (mmm) cc_final: 0.8207 (mmm) REVERT: D 185 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8245 (mp0) REVERT: D 240 LEU cc_start: 0.9550 (mm) cc_final: 0.9259 (pp) REVERT: D 282 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8781 (mm-40) REVERT: D 353 PHE cc_start: 0.9233 (t80) cc_final: 0.8938 (t80) REVERT: E 34 MET cc_start: 0.7962 (tpp) cc_final: 0.7740 (tpp) REVERT: E 75 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8679 (ttm-80) REVERT: E 101 LEU cc_start: 0.8960 (tp) cc_final: 0.8698 (tp) REVERT: E 179 MET cc_start: 0.8817 (tpp) cc_final: 0.8482 (mmm) outliers start: 31 outliers final: 9 residues processed: 198 average time/residue: 0.1039 time to fit residues: 32.2435 Evaluate side-chains 164 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 167 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.032168 restraints weight = 91307.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.033308 restraints weight = 53316.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.034099 restraints weight = 35990.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.034645 restraints weight = 27188.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.035060 restraints weight = 21924.121| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14255 Z= 0.135 Angle : 0.732 12.958 19470 Z= 0.354 Chirality : 0.043 0.159 2300 Planarity : 0.004 0.038 2360 Dihedral : 7.343 65.399 2535 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.11 % Allowed : 15.28 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.47 (0.20), residues: 1700 helix: 1.39 (0.22), residues: 575 sheet: 0.44 (0.26), residues: 395 loop : -0.58 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 75 TYR 0.018 0.002 TYR C 144 PHE 0.022 0.001 PHE A 353 TRP 0.006 0.001 TRP B 358 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14245) covalent geometry : angle 0.73183 / 0.35 (19445) SS BOND : bond 0.00064 / 0.03 ( 5) SS BOND : angle 0.28217 / 0.18 ( 10) hydrogen bonds : bond 0.03942 / 2.59 ( 691) hydrogen bonds : angle 4.95691 / 3.38 ( 2418) link_BETA1-4 : bond 0.00682 / 0.39 ( 5) link_BETA1-4 : angle 0.93317 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8106 (tpp) cc_final: 0.7593 (tpp) REVERT: A 82 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: A 101 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (tp) REVERT: A 105 MET cc_start: 0.8951 (mmm) cc_final: 0.8295 (mmm) REVERT: A 156 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8363 (mtp) REVERT: A 179 MET cc_start: 0.8582 (mmm) cc_final: 0.8136 (mmm) REVERT: A 282 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8950 (mm-40) REVERT: A 300 ASP cc_start: 0.9141 (m-30) cc_final: 0.8878 (m-30) REVERT: B 72 MET cc_start: 0.9101 (tpp) cc_final: 0.8666 (tpp) REVERT: B 75 ARG cc_start: 0.9008 (ttm110) cc_final: 0.8796 (ttp80) REVERT: B 101 LEU cc_start: 0.8711 (tp) cc_final: 0.8393 (tp) REVERT: B 105 MET cc_start: 0.8727 (mmt) cc_final: 0.8369 (mmt) REVERT: B 156 MET cc_start: 0.8508 (mtp) cc_final: 0.8189 (mtt) REVERT: B 179 MET cc_start: 0.8952 (tpp) cc_final: 0.8573 (mmm) REVERT: B 244 TYR cc_start: 0.9137 (m-80) cc_final: 0.8899 (m-80) REVERT: C 72 MET cc_start: 0.9126 (tpt) cc_final: 0.8670 (tpp) REVERT: C 75 ARG cc_start: 0.9050 (ttm110) cc_final: 0.8836 (ttp80) REVERT: C 101 LEU cc_start: 0.8844 (tp) cc_final: 0.8586 (tp) REVERT: C 156 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7379 (ptt) REVERT: C 179 MET cc_start: 0.8880 (tpp) cc_final: 0.8437 (mmm) REVERT: C 243 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8716 (mpp) REVERT: C 252 ILE cc_start: 0.9660 (mt) cc_final: 0.9224 (mt) REVERT: C 255 TRP cc_start: 0.8957 (m-10) cc_final: 0.8293 (m-10) REVERT: C 282 GLN cc_start: 0.9402 (mm-40) cc_final: 0.9055 (mm-40) REVERT: C 300 ASP cc_start: 0.9269 (m-30) cc_final: 0.8949 (m-30) REVERT: D 34 MET cc_start: 0.8441 (tpp) cc_final: 0.8209 (tpp) REVERT: D 72 MET cc_start: 0.9075 (tpt) cc_final: 0.8822 (tpt) REVERT: D 101 LEU cc_start: 0.8995 (tp) cc_final: 0.8740 (tp) REVERT: D 105 MET cc_start: 0.8893 (mmm) cc_final: 0.8225 (mmm) REVERT: D 244 TYR cc_start: 0.9121 (m-80) cc_final: 0.8915 (m-80) REVERT: D 255 TRP cc_start: 0.8809 (m-10) cc_final: 0.8390 (m-10) REVERT: D 279 MET cc_start: 0.9278 (tpp) cc_final: 0.8967 (tpt) REVERT: D 282 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8774 (mm-40) REVERT: D 353 PHE cc_start: 0.9248 (t80) cc_final: 0.8960 (t80) REVERT: E 34 MET cc_start: 0.7968 (tpp) cc_final: 0.7742 (tpp) REVERT: E 75 ARG cc_start: 0.9084 (ttm110) cc_final: 0.8676 (ttm-80) REVERT: E 101 LEU cc_start: 0.8909 (tp) cc_final: 0.8648 (tp) REVERT: E 152 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8782 (mm) REVERT: E 179 MET cc_start: 0.8778 (tpp) cc_final: 0.8550 (mmm) REVERT: E 278 THR cc_start: 0.9225 (p) cc_final: 0.9017 (t) outliers start: 30 outliers final: 16 residues processed: 184 average time/residue: 0.1078 time to fit residues: 30.8959 Evaluate side-chains 170 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS B 131 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.030565 restraints weight = 94995.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.031653 restraints weight = 55267.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.032432 restraints weight = 37697.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.033018 restraints weight = 28260.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033450 restraints weight = 22623.008| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14255 Z= 0.237 Angle : 0.782 12.518 19470 Z= 0.385 Chirality : 0.044 0.202 2300 Planarity : 0.005 0.050 2360 Dihedral : 7.565 60.860 2535 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.82 % Allowed : 15.56 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.55 (0.21), residues: 1700 helix: 1.45 (0.22), residues: 555 sheet: 0.14 (0.25), residues: 400 loop : -0.25 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 81 TYR 0.024 0.002 TYR B 361 PHE 0.022 0.002 PHE A 353 TRP 0.052 0.001 TRP A 255 HIS 0.005 0.002 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (14245) covalent geometry : angle 0.78097 / 0.38 (19445) SS BOND : bond 0.00064 / 0.03 ( 5) SS BOND : angle 0.40748 / 0.23 ( 10) hydrogen bonds : bond 0.04227 / 2.76 ( 691) hydrogen bonds : angle 5.19705 / 3.56 ( 2418) link_BETA1-4 : bond 0.00723 / 0.41 ( 5) link_BETA1-4 : angle 1.74664 / 1.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: A 101 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8696 (tp) REVERT: A 105 MET cc_start: 0.8958 (mmm) cc_final: 0.8242 (mmm) REVERT: A 156 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: A 249 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9383 (tp) REVERT: A 282 GLN cc_start: 0.9324 (mm-40) cc_final: 0.9025 (mm-40) REVERT: A 300 ASP cc_start: 0.9128 (m-30) cc_final: 0.8868 (m-30) REVERT: B 72 MET cc_start: 0.9016 (tpp) cc_final: 0.8471 (tpp) REVERT: B 75 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8737 (ttp80) REVERT: B 101 LEU cc_start: 0.8721 (tp) cc_final: 0.8419 (tp) REVERT: B 156 MET cc_start: 0.8465 (mtp) cc_final: 0.7849 (mtt) REVERT: B 179 MET cc_start: 0.9001 (tpp) cc_final: 0.8669 (mmm) REVERT: B 244 TYR cc_start: 0.9037 (m-80) cc_final: 0.8788 (m-80) REVERT: C 72 MET cc_start: 0.9093 (tpt) cc_final: 0.8593 (tpp) REVERT: C 101 LEU cc_start: 0.8800 (tp) cc_final: 0.8476 (tp) REVERT: C 179 MET cc_start: 0.8999 (tpp) cc_final: 0.8545 (mmm) REVERT: C 243 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8719 (mpp) REVERT: C 252 ILE cc_start: 0.9672 (mt) cc_final: 0.9210 (mt) REVERT: C 255 TRP cc_start: 0.9044 (m-10) cc_final: 0.8432 (m-10) REVERT: C 282 GLN cc_start: 0.9464 (mm-40) cc_final: 0.9104 (mm-40) REVERT: D 34 MET cc_start: 0.8421 (tpp) cc_final: 0.8061 (tpp) REVERT: D 72 MET cc_start: 0.9062 (tpt) cc_final: 0.8629 (tpp) REVERT: D 101 LEU cc_start: 0.8956 (tp) cc_final: 0.8722 (tp) REVERT: D 105 MET cc_start: 0.8910 (mmm) cc_final: 0.8359 (mmm) REVERT: D 255 TRP cc_start: 0.8853 (m-10) cc_final: 0.8443 (m-10) REVERT: D 282 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8859 (mm-40) REVERT: D 353 PHE cc_start: 0.9229 (t80) cc_final: 0.8979 (t80) REVERT: E 34 MET cc_start: 0.8008 (tpp) cc_final: 0.7787 (tpp) REVERT: E 72 MET cc_start: 0.8944 (tpp) cc_final: 0.8703 (tpp) REVERT: E 75 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8826 (ttp80) REVERT: E 152 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8802 (mm) REVERT: E 300 ASP cc_start: 0.9271 (m-30) cc_final: 0.8972 (m-30) outliers start: 40 outliers final: 19 residues processed: 183 average time/residue: 0.0968 time to fit residues: 28.3202 Evaluate side-chains 160 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 131 ASN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.030675 restraints weight = 95300.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.031747 restraints weight = 55752.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.032510 restraints weight = 38138.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.033045 restraints weight = 28512.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033446 restraints weight = 22994.234| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 14255 Z= 0.215 Angle : 0.784 15.832 19470 Z= 0.383 Chirality : 0.044 0.208 2300 Planarity : 0.004 0.047 2360 Dihedral : 7.485 59.386 2535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.46 % Allowed : 17.32 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.21 (0.21), residues: 1700 helix: 1.22 (0.22), residues: 600 sheet: 0.05 (0.26), residues: 405 loop : -0.69 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 81 TYR 0.020 0.002 TYR B 361 PHE 0.021 0.002 PHE A 353 TRP 0.026 0.001 TRP A 255 HIS 0.005 0.002 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (14245) covalent geometry : angle 0.78268 / 0.38 (19445) SS BOND : bond 0.00062 / 0.04 ( 5) SS BOND : angle 0.41577 / 0.27 ( 10) hydrogen bonds : bond 0.04007 / 2.62 ( 691) hydrogen bonds : angle 5.20529 / 3.56 ( 2418) link_BETA1-4 : bond 0.00600 / 0.36 ( 5) link_BETA1-4 : angle 1.65208 / 0.99 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8254 (tpp) cc_final: 0.7916 (tpp) REVERT: A 82 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: A 101 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (tp) REVERT: A 105 MET cc_start: 0.8940 (mmm) cc_final: 0.8429 (mmm) REVERT: A 156 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: A 166 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8205 (tp40) REVERT: A 249 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9438 (tp) REVERT: A 282 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9003 (mm-40) REVERT: A 300 ASP cc_start: 0.9184 (m-30) cc_final: 0.8854 (m-30) REVERT: B 72 MET cc_start: 0.8986 (tpp) cc_final: 0.8396 (tpp) REVERT: B 101 LEU cc_start: 0.8691 (tp) cc_final: 0.8347 (tp) REVERT: B 156 MET cc_start: 0.8448 (mtp) cc_final: 0.7792 (mtt) REVERT: B 179 MET cc_start: 0.9004 (tpp) cc_final: 0.8685 (mmm) REVERT: C 72 MET cc_start: 0.9069 (tpt) cc_final: 0.8505 (tpp) REVERT: C 101 LEU cc_start: 0.8856 (tp) cc_final: 0.8507 (tp) REVERT: C 179 MET cc_start: 0.9004 (tpp) cc_final: 0.8570 (mmm) REVERT: C 282 GLN cc_start: 0.9475 (mm-40) cc_final: 0.9132 (mm-40) REVERT: D 72 MET cc_start: 0.9091 (tpt) cc_final: 0.8645 (tpp) REVERT: D 101 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (tp) REVERT: D 105 MET cc_start: 0.8891 (mmm) cc_final: 0.8344 (mmm) REVERT: D 244 TYR cc_start: 0.9177 (m-80) cc_final: 0.8946 (m-80) REVERT: D 255 TRP cc_start: 0.8850 (m-10) cc_final: 0.8469 (m-10) REVERT: D 279 MET cc_start: 0.9286 (tpp) cc_final: 0.8997 (tpt) REVERT: D 282 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8868 (mm-40) REVERT: D 353 PHE cc_start: 0.9248 (t80) cc_final: 0.9015 (t80) REVERT: E 72 MET cc_start: 0.8965 (tpp) cc_final: 0.8588 (tpp) REVERT: E 75 ARG cc_start: 0.9064 (ttm110) cc_final: 0.8828 (ttp80) REVERT: E 152 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8804 (mm) REVERT: E 300 ASP cc_start: 0.9252 (m-30) cc_final: 0.8935 (m-30) REVERT: E 353 PHE cc_start: 0.9205 (t80) cc_final: 0.8998 (t80) outliers start: 35 outliers final: 20 residues processed: 163 average time/residue: 0.0969 time to fit residues: 25.0897 Evaluate side-chains 164 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 159 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.039606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.031449 restraints weight = 92940.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.032576 restraints weight = 53644.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.033401 restraints weight = 36015.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033929 restraints weight = 26878.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.034367 restraints weight = 21703.210| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14255 Z= 0.128 Angle : 0.768 13.836 19470 Z= 0.366 Chirality : 0.043 0.179 2300 Planarity : 0.004 0.041 2360 Dihedral : 7.054 59.786 2535 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.90 % Allowed : 17.82 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.52 (0.21), residues: 1700 helix: 1.50 (0.23), residues: 570 sheet: 0.10 (0.25), residues: 405 loop : -0.35 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 75 TYR 0.015 0.001 TYR A 238 PHE 0.020 0.001 PHE A 353 TRP 0.060 0.001 TRP E 255 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14245) covalent geometry : angle 0.76826 / 0.37 (19445) SS BOND : bond 0.00055 / 0.04 ( 5) SS BOND : angle 0.40612 / 0.30 ( 10) hydrogen bonds : bond 0.03675 / 2.42 ( 691) hydrogen bonds : angle 4.93039 / 3.38 ( 2418) link_BETA1-4 : bond 0.00642 / 0.35 ( 5) link_BETA1-4 : angle 1.01991 / 0.60 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8095 (tpp) cc_final: 0.7830 (tpp) REVERT: A 82 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: A 249 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9355 (mm) REVERT: A 282 GLN cc_start: 0.9341 (mm-40) cc_final: 0.9009 (mm-40) REVERT: A 300 ASP cc_start: 0.9171 (m-30) cc_final: 0.8823 (m-30) REVERT: B 72 MET cc_start: 0.9051 (tpp) cc_final: 0.8422 (tpp) REVERT: B 101 LEU cc_start: 0.8736 (tp) cc_final: 0.8377 (tp) REVERT: B 105 MET cc_start: 0.8774 (mmt) cc_final: 0.8475 (mmt) REVERT: B 156 MET cc_start: 0.8548 (mtp) cc_final: 0.7873 (mtt) REVERT: B 179 MET cc_start: 0.9013 (tpp) cc_final: 0.8707 (mmm) REVERT: B 253 LEU cc_start: 0.9651 (mm) cc_final: 0.9421 (mt) REVERT: B 292 LYS cc_start: 0.8986 (mttt) cc_final: 0.8636 (mtmm) REVERT: C 72 MET cc_start: 0.9037 (tpt) cc_final: 0.8536 (tpp) REVERT: C 101 LEU cc_start: 0.8860 (tp) cc_final: 0.8548 (tp) REVERT: C 179 MET cc_start: 0.8955 (tpp) cc_final: 0.8627 (mmm) REVERT: C 282 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9072 (mm-40) REVERT: C 300 ASP cc_start: 0.9251 (m-30) cc_final: 0.8885 (m-30) REVERT: D 34 MET cc_start: 0.8258 (tpp) cc_final: 0.8004 (tpp) REVERT: D 72 MET cc_start: 0.9074 (tpt) cc_final: 0.8630 (tpp) REVERT: D 101 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8683 (tp) REVERT: D 105 MET cc_start: 0.8873 (mmm) cc_final: 0.8360 (mmm) REVERT: D 255 TRP cc_start: 0.8792 (m-10) cc_final: 0.8377 (m-10) REVERT: D 282 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8830 (mm-40) REVERT: D 353 PHE cc_start: 0.9233 (t80) cc_final: 0.9024 (t80) REVERT: E 72 MET cc_start: 0.9011 (tpp) cc_final: 0.8704 (tpp) REVERT: E 75 ARG cc_start: 0.9058 (ttm110) cc_final: 0.8714 (ttm110) REVERT: E 152 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8858 (mm) REVERT: E 300 ASP cc_start: 0.9249 (m-30) cc_final: 0.8896 (m-30) REVERT: E 353 PHE cc_start: 0.9192 (t80) cc_final: 0.8980 (t80) outliers start: 27 outliers final: 14 residues processed: 169 average time/residue: 0.0952 time to fit residues: 25.5678 Evaluate side-chains 158 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.031045 restraints weight = 96581.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.032154 restraints weight = 55982.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032947 restraints weight = 37584.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033485 restraints weight = 28028.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.033879 restraints weight = 22386.541| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14255 Z= 0.215 Angle : 0.790 13.307 19470 Z= 0.384 Chirality : 0.043 0.219 2300 Planarity : 0.004 0.045 2360 Dihedral : 7.268 58.836 2535 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 18.52 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.15 (0.21), residues: 1700 helix: 1.29 (0.22), residues: 605 sheet: -0.04 (0.26), residues: 390 loop : -0.81 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 81 TYR 0.019 0.002 TYR B 238 PHE 0.019 0.002 PHE A 353 TRP 0.053 0.002 TRP E 255 HIS 0.005 0.002 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (14245) covalent geometry : angle 0.78946 / 0.38 (19445) SS BOND : bond 0.00103 / 0.05 ( 5) SS BOND : angle 0.37217 / 0.26 ( 10) hydrogen bonds : bond 0.03942 / 2.58 ( 691) hydrogen bonds : angle 5.08108 / 3.48 ( 2418) link_BETA1-4 : bond 0.00688 / 0.41 ( 5) link_BETA1-4 : angle 1.67078 / 1.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8233 (tpp) cc_final: 0.7890 (tpp) REVERT: A 82 GLN cc_start: 0.8955 (mp10) cc_final: 0.8646 (mp10) REVERT: A 105 MET cc_start: 0.8859 (mmm) cc_final: 0.8585 (mmm) REVERT: A 282 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9020 (mm-40) REVERT: A 300 ASP cc_start: 0.9179 (m-30) cc_final: 0.8845 (m-30) REVERT: B 72 MET cc_start: 0.8993 (tpp) cc_final: 0.8326 (tpp) REVERT: B 101 LEU cc_start: 0.8728 (tp) cc_final: 0.8423 (tp) REVERT: B 156 MET cc_start: 0.8470 (mtp) cc_final: 0.7786 (mtt) REVERT: B 179 MET cc_start: 0.8971 (tpp) cc_final: 0.8732 (mmm) REVERT: B 279 MET cc_start: 0.9071 (tpt) cc_final: 0.8869 (tpp) REVERT: B 292 LYS cc_start: 0.8958 (mttt) cc_final: 0.8546 (mtmm) REVERT: C 72 MET cc_start: 0.9072 (tpt) cc_final: 0.8527 (tpp) REVERT: C 101 LEU cc_start: 0.8874 (tp) cc_final: 0.8537 (tp) REVERT: C 179 MET cc_start: 0.8996 (tpp) cc_final: 0.8615 (mmm) REVERT: C 282 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9099 (mm-40) REVERT: D 34 MET cc_start: 0.8322 (tpp) cc_final: 0.8071 (tpp) REVERT: D 72 MET cc_start: 0.9072 (tpt) cc_final: 0.8622 (tpp) REVERT: D 101 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8610 (tp) REVERT: D 105 MET cc_start: 0.8935 (mmm) cc_final: 0.8422 (mmm) REVERT: D 255 TRP cc_start: 0.8838 (m-10) cc_final: 0.8437 (m-10) REVERT: D 353 PHE cc_start: 0.9231 (t80) cc_final: 0.9001 (t80) REVERT: E 72 MET cc_start: 0.9007 (tpp) cc_final: 0.8661 (tpp) REVERT: E 152 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8791 (mm) REVERT: E 179 MET cc_start: 0.8674 (mmm) cc_final: 0.8422 (mmt) REVERT: E 300 ASP cc_start: 0.9241 (m-30) cc_final: 0.8916 (m-30) REVERT: E 353 PHE cc_start: 0.9190 (t80) cc_final: 0.8984 (t80) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 0.0900 time to fit residues: 23.2009 Evaluate side-chains 157 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 58 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.032037 restraints weight = 93561.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.033170 restraints weight = 53716.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.034034 restraints weight = 35908.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034596 restraints weight = 26755.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.035009 restraints weight = 21335.526| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14255 Z= 0.130 Angle : 0.788 14.231 19470 Z= 0.373 Chirality : 0.043 0.200 2300 Planarity : 0.004 0.040 2360 Dihedral : 6.811 58.766 2535 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.27 % Allowed : 19.08 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.48 (0.21), residues: 1700 helix: 1.54 (0.22), residues: 575 sheet: 0.08 (0.26), residues: 400 loop : -0.46 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.014 0.001 TYR A 238 PHE 0.019 0.001 PHE A 353 TRP 0.052 0.001 TRP E 255 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14245) covalent geometry : angle 0.78825 / 0.37 (19445) SS BOND : bond 0.00091 / 0.06 ( 5) SS BOND : angle 0.47086 / 0.35 ( 10) hydrogen bonds : bond 0.03583 / 2.38 ( 691) hydrogen bonds : angle 4.74686 / 3.24 ( 2418) link_BETA1-4 : bond 0.00649 / 0.39 ( 5) link_BETA1-4 : angle 0.73779 / 0.44 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8165 (tpp) cc_final: 0.7777 (tpp) REVERT: A 82 GLN cc_start: 0.8795 (mp10) cc_final: 0.8587 (mp10) REVERT: A 105 MET cc_start: 0.8786 (mmm) cc_final: 0.8356 (mmt) REVERT: A 126 GLU cc_start: 0.8862 (mp0) cc_final: 0.8590 (tp30) REVERT: A 282 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8998 (mm-40) REVERT: A 300 ASP cc_start: 0.9175 (m-30) cc_final: 0.8832 (m-30) REVERT: B 72 MET cc_start: 0.9035 (tpp) cc_final: 0.8465 (tpp) REVERT: B 101 LEU cc_start: 0.8740 (tp) cc_final: 0.8387 (tp) REVERT: B 105 MET cc_start: 0.8663 (mmt) cc_final: 0.8441 (mmt) REVERT: B 156 MET cc_start: 0.8593 (mtp) cc_final: 0.8124 (mtt) REVERT: B 179 MET cc_start: 0.8958 (tpp) cc_final: 0.8739 (mmm) REVERT: B 243 MET cc_start: 0.9107 (mmm) cc_final: 0.8776 (mpp) REVERT: B 279 MET cc_start: 0.9035 (tpt) cc_final: 0.8823 (tpp) REVERT: B 292 LYS cc_start: 0.8987 (mttt) cc_final: 0.8669 (mtmm) REVERT: C 72 MET cc_start: 0.9041 (tpt) cc_final: 0.8511 (tpp) REVERT: C 101 LEU cc_start: 0.8897 (tp) cc_final: 0.8549 (tp) REVERT: C 179 MET cc_start: 0.8951 (tpp) cc_final: 0.8692 (mmm) REVERT: C 282 GLN cc_start: 0.9475 (mm-40) cc_final: 0.9021 (mm-40) REVERT: C 300 ASP cc_start: 0.9282 (m-30) cc_final: 0.8927 (m-30) REVERT: D 34 MET cc_start: 0.8331 (tpp) cc_final: 0.8053 (tpp) REVERT: D 72 MET cc_start: 0.9090 (tpt) cc_final: 0.8719 (tpp) REVERT: D 101 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8644 (tp) REVERT: D 105 MET cc_start: 0.8853 (mmm) cc_final: 0.8357 (mmm) REVERT: D 255 TRP cc_start: 0.8741 (m-10) cc_final: 0.8308 (m-10) REVERT: D 282 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8811 (mm-40) REVERT: D 353 PHE cc_start: 0.9233 (t80) cc_final: 0.8989 (t80) REVERT: E 72 MET cc_start: 0.8994 (tpp) cc_final: 0.8656 (tpp) REVERT: E 152 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8868 (mm) REVERT: E 282 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8732 (mm-40) REVERT: E 300 ASP cc_start: 0.9229 (m-30) cc_final: 0.8857 (m-30) REVERT: E 302 TRP cc_start: 0.9389 (t-100) cc_final: 0.8810 (t60) REVERT: E 353 PHE cc_start: 0.9188 (t80) cc_final: 0.8956 (t80) outliers start: 18 outliers final: 11 residues processed: 170 average time/residue: 0.0949 time to fit residues: 26.0776 Evaluate side-chains 152 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 36 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 131 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.039324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.031497 restraints weight = 96616.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.032592 restraints weight = 56081.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.033385 restraints weight = 38190.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033940 restraints weight = 28329.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.034364 restraints weight = 22416.369| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14255 Z= 0.209 Angle : 0.812 13.787 19470 Z= 0.391 Chirality : 0.044 0.251 2300 Planarity : 0.005 0.045 2360 Dihedral : 7.040 56.302 2535 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.48 % Allowed : 19.58 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.20 (0.21), residues: 1700 helix: 1.36 (0.22), residues: 605 sheet: -0.01 (0.26), residues: 400 loop : -0.82 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 75 TYR 0.019 0.002 TYR B 361 PHE 0.018 0.002 PHE A 353 TRP 0.045 0.001 TRP E 255 HIS 0.005 0.002 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (14245) covalent geometry : angle 0.81089 / 0.39 (19445) SS BOND : bond 0.00143 / 0.07 ( 5) SS BOND : angle 0.37278 / 0.27 ( 10) hydrogen bonds : bond 0.03825 / 2.51 ( 691) hydrogen bonds : angle 4.97572 / 3.40 ( 2418) link_BETA1-4 : bond 0.00755 / 0.41 ( 5) link_BETA1-4 : angle 1.76051 / 1.05 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.44 seconds wall clock time: 34 minutes 49.93 seconds (2089.93 seconds total)