Starting phenix.real_space_refine on Thu Jun 12 12:20:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_6346.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_6346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_6346.map" model { file = "/net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_6346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jaf_6346/06_2025/3jaf_6346.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 8.01, per 1000 atoms: 0.58 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.70 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: 4.36 Time building geometry restraints manager: 3.93 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: 8605 24.30 - 48.59: 220 48.59 - 72.89: 75 72.89 - 97.19: 40 97.19 - 121.48: 85 Dihedral angle restraints: 9025 sinusoidal: 3975 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 9022 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.080 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 18.829 121.482 5740 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.023 0.003 TRP D 259 HIS 0.003 0.001 HIS B 125 PHE 0.029 0.004 PHE E 29 TYR 0.026 0.003 TYR E 94 ARG 0.021 0.003 ARG C 229 Details of bonding type rmsd link_BETA1-4 : bond 0.01909 ( 5) link_BETA1-4 : angle 0.65823 ( 15) hydrogen bonds : bond 0.14404 ( 691) hydrogen bonds : angle 9.58881 ( 2418) SS BOND : bond 0.00709 ( 5) SS BOND : angle 0.46132 ( 10) covalent geometry : bond 0.00630 (14245) covalent geometry : angle 1.34460 (19445) *********************** 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 : 2.631 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: 0.6700 (t0) REVERT: E 89 LEU cc_start: 0.8164 (mt) cc_final: 0.7917 (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: 0.2942 time to fit residues: 143.3679 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 : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0170 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 133 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 131 ASN A 354 ASN B 54 ASN B 131 ASN B 354 ASN C 54 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.031526 restraints weight = 95144.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.032622 restraints weight = 55049.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.033443 restraints weight = 37301.826| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14255 Z= 0.209 Angle : 0.877 8.793 19470 Z= 0.428 Chirality : 0.051 0.385 2300 Planarity : 0.006 0.049 2360 Dihedral : 13.196 88.632 2745 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.61 % Allowed : 8.52 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1700 helix: 0.60 (0.20), residues: 575 sheet: 0.81 (0.25), residues: 380 loop : -0.54 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.004 0.001 HIS D 125 PHE 0.028 0.002 PHE D 353 TYR 0.019 0.002 TYR C 144 ARG 0.007 0.001 ARG E 212 Details of bonding type rmsd link_BETA1-4 : bond 0.01206 ( 5) link_BETA1-4 : angle 0.67178 ( 15) hydrogen bonds : bond 0.04981 ( 691) hydrogen bonds : angle 6.26004 ( 2418) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.32123 ( 10) covalent geometry : bond 0.00463 (14245) covalent geometry : angle 0.87772 (19445) *********************** 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 236 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 2.099 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: 0.9148 (ttm110) cc_final: 0.8874 (ttp80) REVERT: A 152 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8639 (mm) REVERT: A 156 MET cc_start: 0.8537 (ptp) cc_final: 0.8255 (mtp) REVERT: B 105 MET cc_start: 0.9009 (mmt) cc_final: 0.8610 (mmt) REVERT: C 72 MET cc_start: 0.9035 (tpt) cc_final: 0.8589 (tpp) REVERT: C 94 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.7086 (m-10) REVERT: C 152 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8805 (mm) REVERT: C 156 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6975 (ptt) REVERT: C 163 MET cc_start: 0.8896 (pmm) cc_final: 0.8671 (pmm) REVERT: C 235 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: C 240 LEU cc_start: 0.9470 (mp) cc_final: 0.9222 (pp) REVERT: C 278 THR cc_start: 0.9345 (p) cc_final: 0.9112 (p) REVERT: C 282 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8945 (mm-40) REVERT: D 34 MET cc_start: 0.8096 (tpp) cc_final: 0.7697 (tpp) REVERT: D 72 MET cc_start: 0.8844 (tpt) cc_final: 0.8586 (tpt) REVERT: D 152 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8912 (mm) REVERT: D 278 THR cc_start: 0.9275 (p) cc_final: 0.8594 (t) REVERT: D 282 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8765 (mm-40) REVERT: E 89 LEU cc_start: 0.9335 (mt) cc_final: 0.8961 (mt) REVERT: E 152 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8642 (mm) REVERT: E 163 MET cc_start: 0.8920 (pmm) cc_final: 0.8608 (pmm) REVERT: E 179 MET cc_start: 0.8901 (tpp) cc_final: 0.8469 (mmm) REVERT: E 278 THR cc_start: 0.9198 (p) cc_final: 0.8902 (t) outliers start: 37 outliers final: 9 residues processed: 220 average time/residue: 0.2769 time to fit residues: 95.7242 Evaluate side-chains 170 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 152 LEU 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 152 LEU Chi-restraints excluded: chain D residue 243 MET 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 139 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** 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 = 0.039810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.031651 restraints weight = 93937.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.032801 restraints weight = 54790.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.033636 restraints weight = 36954.777| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14255 Z= 0.146 Angle : 0.756 12.169 19470 Z= 0.370 Chirality : 0.044 0.200 2300 Planarity : 0.004 0.044 2360 Dihedral : 10.483 72.744 2745 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.62 % Allowed : 13.17 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1700 helix: 1.13 (0.21), residues: 575 sheet: 0.78 (0.26), residues: 380 loop : -0.51 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 259 HIS 0.002 0.001 HIS D 125 PHE 0.021 0.002 PHE E 353 TYR 0.024 0.002 TYR C 144 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd link_BETA1-4 : bond 0.00771 ( 5) link_BETA1-4 : angle 0.74430 ( 15) hydrogen bonds : bond 0.04398 ( 691) hydrogen bonds : angle 5.56834 ( 2418) SS BOND : bond 0.00100 ( 5) SS BOND : angle 0.39408 ( 10) covalent geometry : bond 0.00317 (14245) covalent geometry : angle 0.75623 (19445) *********************** 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 208 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.476 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: A 101 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8697 (tp) REVERT: A 105 MET cc_start: 0.8966 (mmm) cc_final: 0.8283 (mmm) REVERT: A 156 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8385 (mtp) REVERT: A 282 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8856 (mm-40) REVERT: A 346 PHE cc_start: 0.8731 (m-80) cc_final: 0.8372 (m-80) REVERT: B 72 MET cc_start: 0.9051 (tpp) cc_final: 0.8808 (tpp) REVERT: B 101 LEU cc_start: 0.8667 (tp) cc_final: 0.8361 (tp) REVERT: B 179 MET cc_start: 0.9024 (tpp) cc_final: 0.8798 (tpp) REVERT: B 300 ASP cc_start: 0.9269 (m-30) cc_final: 0.9010 (m-30) REVERT: B 303 MET cc_start: 0.9583 (mmm) cc_final: 0.9370 (mmm) REVERT: C 72 MET cc_start: 0.9042 (tpt) cc_final: 0.8589 (tpp) REVERT: C 101 LEU cc_start: 0.8816 (tp) cc_final: 0.8571 (tp) REVERT: C 179 MET cc_start: 0.8885 (tpp) cc_final: 0.8354 (mmm) REVERT: C 235 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8449 (mm110) REVERT: C 282 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8975 (mm-40) REVERT: D 34 MET cc_start: 0.8249 (tpp) cc_final: 0.7966 (tpp) REVERT: D 72 MET cc_start: 0.8973 (tpt) cc_final: 0.8670 (tpp) REVERT: D 101 LEU cc_start: 0.8906 (tp) cc_final: 0.8630 (tp) REVERT: D 105 MET cc_start: 0.8822 (mmt) cc_final: 0.8359 (mmt) REVERT: D 152 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8861 (mm) REVERT: D 156 MET cc_start: 0.7624 (ptt) cc_final: 0.6995 (ptt) REVERT: D 278 THR cc_start: 0.9135 (p) cc_final: 0.8514 (t) REVERT: D 282 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8792 (mm-40) REVERT: E 75 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8721 (ttm-80) REVERT: E 89 LEU cc_start: 0.9391 (mt) cc_final: 0.9111 (mt) REVERT: E 101 LEU cc_start: 0.8974 (tp) cc_final: 0.8723 (tp) REVERT: E 179 MET cc_start: 0.8881 (tpp) cc_final: 0.8521 (mmm) REVERT: E 236 MET cc_start: 0.8172 (mmp) cc_final: 0.7910 (ptt) REVERT: E 249 LEU cc_start: 0.9307 (mt) cc_final: 0.9074 (mt) REVERT: E 278 THR cc_start: 0.9249 (p) cc_final: 0.9004 (t) outliers start: 23 outliers final: 11 residues processed: 197 average time/residue: 0.2209 time to fit residues: 67.4041 Evaluate side-chains 173 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 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 249 LEU 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 100 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 271 LEU 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 243 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 64 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 131 ASN D 166 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.030748 restraints weight = 96274.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031857 restraints weight = 56011.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.032662 restraints weight = 38197.192| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14255 Z= 0.213 Angle : 0.760 11.048 19470 Z= 0.375 Chirality : 0.044 0.209 2300 Planarity : 0.005 0.044 2360 Dihedral : 8.924 68.142 2745 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.46 % Allowed : 14.79 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1700 helix: 1.49 (0.22), residues: 560 sheet: 0.55 (0.26), residues: 385 loop : -0.41 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.014 0.002 HIS D 217 PHE 0.018 0.002 PHE D 353 TYR 0.020 0.002 TYR D 238 ARG 0.006 0.001 ARG C 75 Details of bonding type rmsd link_BETA1-4 : bond 0.00608 ( 5) link_BETA1-4 : angle 1.63501 ( 15) hydrogen bonds : bond 0.04266 ( 691) hydrogen bonds : angle 5.31564 ( 2418) SS BOND : bond 0.00025 ( 5) SS BOND : angle 0.39054 ( 10) covalent geometry : bond 0.00462 (14245) covalent geometry : angle 0.75919 (19445) *********************** 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 203 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.810 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: A 34 MET cc_start: 0.8260 (tpp) cc_final: 0.7901 (tpp) REVERT: A 101 LEU cc_start: 0.9042 (tp) cc_final: 0.8732 (tp) REVERT: A 105 MET cc_start: 0.9034 (mmm) cc_final: 0.8352 (mmm) REVERT: A 156 MET cc_start: 0.8610 (ptp) cc_final: 0.8396 (mtp) REVERT: A 282 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8927 (mm-40) REVERT: B 72 MET cc_start: 0.9088 (tpp) cc_final: 0.8863 (tpp) REVERT: B 101 LEU cc_start: 0.8686 (tp) cc_final: 0.8350 (tp) REVERT: B 244 TYR cc_start: 0.9160 (m-80) cc_final: 0.8772 (m-80) REVERT: B 300 ASP cc_start: 0.9272 (m-30) cc_final: 0.8928 (m-30) REVERT: C 72 MET cc_start: 0.9121 (tpt) cc_final: 0.8760 (tpt) REVERT: C 101 LEU cc_start: 0.8776 (tp) cc_final: 0.8491 (tp) REVERT: C 179 MET cc_start: 0.8982 (tpp) cc_final: 0.8421 (mmm) REVERT: C 282 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9048 (mm-40) REVERT: D 72 MET cc_start: 0.8995 (tpt) cc_final: 0.8737 (tpt) REVERT: D 101 LEU cc_start: 0.8972 (tp) cc_final: 0.8653 (tp) REVERT: D 105 MET cc_start: 0.8848 (mmt) cc_final: 0.8386 (mmt) REVERT: D 152 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 235 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8352 (mm110) REVERT: E 34 MET cc_start: 0.7967 (tpp) cc_final: 0.7706 (tpp) REVERT: E 75 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8720 (ttm-80) REVERT: E 89 LEU cc_start: 0.9334 (mt) cc_final: 0.8922 (mt) REVERT: E 101 LEU cc_start: 0.8940 (tp) cc_final: 0.8659 (tp) REVERT: E 152 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8771 (mm) REVERT: E 179 MET cc_start: 0.8879 (tpp) cc_final: 0.8502 (mmm) REVERT: E 303 MET cc_start: 0.9550 (mmm) cc_final: 0.9350 (mmm) outliers start: 35 outliers final: 19 residues processed: 191 average time/residue: 0.2596 time to fit residues: 77.2905 Evaluate side-chains 167 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 235 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** 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 = 0.2840 r_free = 0.2840 target = 0.039807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031681 restraints weight = 91715.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.032805 restraints weight = 53101.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033606 restraints weight = 35809.633| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14255 Z= 0.139 Angle : 0.738 14.223 19470 Z= 0.356 Chirality : 0.043 0.163 2300 Planarity : 0.004 0.038 2360 Dihedral : 8.224 66.255 2745 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.97 % Allowed : 15.99 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1700 helix: 1.38 (0.22), residues: 575 sheet: 0.47 (0.25), residues: 395 loop : -0.63 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP E 255 HIS 0.002 0.001 HIS B 125 PHE 0.037 0.001 PHE D 353 TYR 0.017 0.001 TYR A 144 ARG 0.004 0.000 ARG A 75 Details of bonding type rmsd link_BETA1-4 : bond 0.00712 ( 5) link_BETA1-4 : angle 1.20933 ( 15) hydrogen bonds : bond 0.03998 ( 691) hydrogen bonds : angle 5.06358 ( 2418) SS BOND : bond 0.00079 ( 5) SS BOND : angle 0.35239 ( 10) covalent geometry : bond 0.00308 (14245) covalent geometry : angle 0.73811 (19445) *********************** 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: 28 poor density : 168 time to evaluate : 1.546 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: A 34 MET cc_start: 0.8343 (tpp) cc_final: 0.7832 (tpp) REVERT: A 82 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: A 101 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8702 (tp) REVERT: A 105 MET cc_start: 0.9025 (mmm) cc_final: 0.8351 (mmm) REVERT: A 156 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8397 (mtp) REVERT: A 179 MET cc_start: 0.8629 (mmm) cc_final: 0.8221 (mmm) REVERT: A 282 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8975 (mm-40) REVERT: B 72 MET cc_start: 0.9124 (tpp) cc_final: 0.8732 (tpp) REVERT: B 101 LEU cc_start: 0.8742 (tp) cc_final: 0.8412 (tp) REVERT: B 156 MET cc_start: 0.8449 (mtp) cc_final: 0.7875 (mtt) REVERT: B 179 MET cc_start: 0.9085 (tpp) cc_final: 0.8487 (mmm) REVERT: B 244 TYR cc_start: 0.9131 (m-80) cc_final: 0.8832 (m-80) REVERT: B 300 ASP cc_start: 0.9321 (m-30) cc_final: 0.8975 (m-30) REVERT: C 72 MET cc_start: 0.9175 (tpt) cc_final: 0.8798 (tpt) REVERT: C 101 LEU cc_start: 0.8826 (tp) cc_final: 0.8533 (tp) REVERT: C 179 MET cc_start: 0.8939 (tpp) cc_final: 0.8449 (mmm) REVERT: C 243 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8694 (mpp) REVERT: C 282 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9027 (mm-40) REVERT: C 300 ASP cc_start: 0.9285 (m-30) cc_final: 0.8966 (m-30) REVERT: D 34 MET cc_start: 0.8525 (tpp) cc_final: 0.8235 (tpp) REVERT: D 72 MET cc_start: 0.9093 (tpt) cc_final: 0.8697 (tpt) REVERT: D 101 LEU cc_start: 0.8972 (tp) cc_final: 0.8648 (tp) REVERT: D 105 MET cc_start: 0.8801 (mmt) cc_final: 0.8381 (mmt) REVERT: D 163 MET cc_start: 0.8677 (pmm) cc_final: 0.8435 (mpp) REVERT: D 235 GLN cc_start: 0.8526 (mm110) cc_final: 0.8307 (mm110) REVERT: E 34 MET cc_start: 0.8002 (tpp) cc_final: 0.7788 (tpp) REVERT: E 75 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8744 (ttm-80) REVERT: E 101 LEU cc_start: 0.8989 (tp) cc_final: 0.8685 (tp) REVERT: E 152 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8754 (mm) REVERT: E 179 MET cc_start: 0.8870 (tpp) cc_final: 0.8539 (mmm) REVERT: E 255 TRP cc_start: 0.9051 (m-90) cc_final: 0.8598 (m-90) REVERT: E 300 ASP cc_start: 0.9326 (m-30) cc_final: 0.8981 (m-30) outliers start: 28 outliers final: 14 residues processed: 181 average time/residue: 0.2077 time to fit residues: 59.0752 Evaluate side-chains 170 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 156 MET 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 B residue 249 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 71 THR 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 100 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.038696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.030635 restraints weight = 97569.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.031746 restraints weight = 55582.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.032590 restraints weight = 37305.113| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14255 Z= 0.204 Angle : 0.762 13.123 19470 Z= 0.370 Chirality : 0.043 0.202 2300 Planarity : 0.004 0.044 2360 Dihedral : 8.325 62.920 2745 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 15.70 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1700 helix: 1.48 (0.23), residues: 555 sheet: 0.29 (0.26), residues: 400 loop : -0.29 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 255 HIS 0.004 0.002 HIS A 217 PHE 0.026 0.002 PHE D 353 TYR 0.020 0.002 TYR B 361 ARG 0.005 0.001 ARG A 287 Details of bonding type rmsd link_BETA1-4 : bond 0.00760 ( 5) link_BETA1-4 : angle 1.65227 ( 15) hydrogen bonds : bond 0.04061 ( 691) hydrogen bonds : angle 5.15019 ( 2418) SS BOND : bond 0.00038 ( 5) SS BOND : angle 0.42829 ( 10) covalent geometry : bond 0.00441 (14245) covalent geometry : angle 0.76112 (19445) *********************** 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 195 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8407 (tpp) cc_final: 0.7905 (tpp) REVERT: A 82 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8584 (mp10) REVERT: A 101 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 105 MET cc_start: 0.9001 (mmm) cc_final: 0.8351 (mmm) REVERT: A 156 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: A 282 GLN cc_start: 0.9313 (mm-40) cc_final: 0.9010 (mm-40) REVERT: B 72 MET cc_start: 0.9047 (tpp) cc_final: 0.8554 (tpp) REVERT: B 101 LEU cc_start: 0.8693 (tp) cc_final: 0.8342 (tp) REVERT: B 156 MET cc_start: 0.8404 (mtp) cc_final: 0.8077 (mtt) REVERT: B 179 MET cc_start: 0.9094 (tpp) cc_final: 0.8575 (mmm) REVERT: B 244 TYR cc_start: 0.9158 (m-80) cc_final: 0.8868 (m-80) REVERT: B 300 ASP cc_start: 0.9307 (m-30) cc_final: 0.8972 (m-30) REVERT: C 72 MET cc_start: 0.9123 (tpt) cc_final: 0.8678 (tpt) REVERT: C 101 LEU cc_start: 0.8832 (tp) cc_final: 0.8522 (tp) REVERT: C 179 MET cc_start: 0.8955 (tpp) cc_final: 0.8533 (mmm) REVERT: C 243 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8799 (mpp) REVERT: C 282 GLN cc_start: 0.9429 (mm-40) cc_final: 0.9054 (mm-40) REVERT: D 34 MET cc_start: 0.8535 (tpp) cc_final: 0.8307 (tpp) REVERT: D 72 MET cc_start: 0.9087 (tpt) cc_final: 0.8776 (tpt) REVERT: D 101 LEU cc_start: 0.9002 (tp) cc_final: 0.8652 (tp) REVERT: D 105 MET cc_start: 0.8801 (mmt) cc_final: 0.8372 (mmt) REVERT: D 171 GLN cc_start: 0.8983 (pt0) cc_final: 0.8673 (pm20) REVERT: E 75 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8883 (ttp80) REVERT: E 152 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8802 (mm) REVERT: E 179 MET cc_start: 0.8876 (tpp) cc_final: 0.8578 (mmm) REVERT: E 255 TRP cc_start: 0.9089 (m-10) cc_final: 0.8743 (m-90) outliers start: 42 outliers final: 20 residues processed: 181 average time/residue: 0.2058 time to fit residues: 59.8791 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 : 1.312 ------------------------------------------------------------------------------- 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 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 249 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 100 ASP 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 Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 85 optimal weight: 0.0870 chunk 159 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 166 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.031312 restraints weight = 95527.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.032466 restraints weight = 54142.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.033300 restraints weight = 36253.573| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14255 Z= 0.141 Angle : 0.752 11.833 19470 Z= 0.362 Chirality : 0.043 0.214 2300 Planarity : 0.004 0.040 2360 Dihedral : 7.920 61.605 2745 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.75 % Allowed : 16.90 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1700 helix: 1.49 (0.22), residues: 575 sheet: 0.27 (0.26), residues: 405 loop : -0.51 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 255 HIS 0.002 0.001 HIS A 125 PHE 0.025 0.001 PHE D 353 TYR 0.015 0.002 TYR C 238 ARG 0.005 0.000 ARG A 81 Details of bonding type rmsd link_BETA1-4 : bond 0.00731 ( 5) link_BETA1-4 : angle 1.33370 ( 15) hydrogen bonds : bond 0.03790 ( 691) hydrogen bonds : angle 4.95270 ( 2418) SS BOND : bond 0.00063 ( 5) SS BOND : angle 0.37809 ( 10) covalent geometry : bond 0.00315 (14245) covalent geometry : angle 0.75136 (19445) *********************** 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 183 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8465 (tpp) cc_final: 0.7996 (tpp) REVERT: A 82 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: A 101 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 105 MET cc_start: 0.9025 (mmm) cc_final: 0.8371 (mmm) REVERT: A 156 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: A 166 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8211 (tp40) REVERT: A 282 GLN cc_start: 0.9304 (mm-40) cc_final: 0.8976 (mm-40) REVERT: B 72 MET cc_start: 0.9043 (tpp) cc_final: 0.8544 (tpp) REVERT: B 101 LEU cc_start: 0.8706 (tp) cc_final: 0.8346 (tp) REVERT: B 156 MET cc_start: 0.8443 (mtp) cc_final: 0.8090 (mtt) REVERT: B 163 MET cc_start: 0.8586 (pmm) cc_final: 0.8315 (mpp) REVERT: B 179 MET cc_start: 0.9032 (tpp) cc_final: 0.8567 (mmm) REVERT: B 244 TYR cc_start: 0.9171 (m-80) cc_final: 0.8868 (m-80) REVERT: B 300 ASP cc_start: 0.9321 (m-30) cc_final: 0.8994 (m-30) REVERT: C 72 MET cc_start: 0.9084 (tpt) cc_final: 0.8652 (tpt) REVERT: C 101 LEU cc_start: 0.8854 (tp) cc_final: 0.8522 (tp) REVERT: C 179 MET cc_start: 0.8991 (tpp) cc_final: 0.8554 (mmm) REVERT: C 243 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8767 (mpp) REVERT: C 282 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9090 (mm-40) REVERT: C 300 ASP cc_start: 0.9288 (m-30) cc_final: 0.8908 (m-30) REVERT: D 72 MET cc_start: 0.9151 (tpt) cc_final: 0.8748 (tpt) REVERT: D 101 LEU cc_start: 0.9031 (tp) cc_final: 0.8672 (tp) REVERT: D 105 MET cc_start: 0.8793 (mmt) cc_final: 0.8404 (mmt) REVERT: D 171 GLN cc_start: 0.9016 (pt0) cc_final: 0.8685 (pm20) REVERT: D 255 TRP cc_start: 0.8858 (m-10) cc_final: 0.8449 (m-10) REVERT: E 75 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8684 (ttm-80) REVERT: E 152 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8824 (mm) REVERT: E 179 MET cc_start: 0.8905 (tpp) cc_final: 0.8634 (mmm) REVERT: E 255 TRP cc_start: 0.8975 (m-10) cc_final: 0.8594 (m-90) REVERT: E 300 ASP cc_start: 0.9322 (m-30) cc_final: 0.8985 (m-30) outliers start: 39 outliers final: 16 residues processed: 169 average time/residue: 0.2176 time to fit residues: 57.9145 Evaluate side-chains 166 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 166 GLN 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 B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 353 PHE 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 100 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 307 LEU 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 Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 149 optimal weight: 0.0000 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.2825 r_free = 0.2825 target = 0.038804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.030866 restraints weight = 96412.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.031992 restraints weight = 55416.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032812 restraints weight = 37256.331| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14255 Z= 0.184 Angle : 0.756 11.134 19470 Z= 0.367 Chirality : 0.044 0.206 2300 Planarity : 0.004 0.043 2360 Dihedral : 7.960 59.812 2745 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1700 helix: 1.50 (0.23), residues: 565 sheet: 0.21 (0.26), residues: 400 loop : -0.42 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 255 HIS 0.003 0.001 HIS A 125 PHE 0.022 0.002 PHE D 353 TYR 0.018 0.002 TYR B 361 ARG 0.006 0.001 ARG A 81 Details of bonding type rmsd link_BETA1-4 : bond 0.00626 ( 5) link_BETA1-4 : angle 1.58257 ( 15) hydrogen bonds : bond 0.03910 ( 691) hydrogen bonds : angle 5.00954 ( 2418) SS BOND : bond 0.00048 ( 5) SS BOND : angle 0.35470 ( 10) covalent geometry : bond 0.00403 (14245) covalent geometry : angle 0.75500 (19445) *********************** 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: 31 poor density : 151 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8461 (tpp) cc_final: 0.8004 (tpp) REVERT: A 82 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8690 (mp10) REVERT: A 101 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8730 (tp) REVERT: A 105 MET cc_start: 0.9012 (mmm) cc_final: 0.8400 (mmm) REVERT: A 156 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: A 249 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9349 (mp) REVERT: A 282 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8993 (mm-40) REVERT: B 72 MET cc_start: 0.9005 (tpp) cc_final: 0.8413 (tpp) REVERT: B 101 LEU cc_start: 0.8676 (tp) cc_final: 0.8332 (tp) REVERT: B 156 MET cc_start: 0.8403 (mtp) cc_final: 0.7739 (mtt) REVERT: B 179 MET cc_start: 0.9016 (tpp) cc_final: 0.8623 (mmm) REVERT: B 244 TYR cc_start: 0.9144 (m-80) cc_final: 0.8873 (m-80) REVERT: B 292 LYS cc_start: 0.8986 (mttt) cc_final: 0.8600 (mtmm) REVERT: B 300 ASP cc_start: 0.9312 (m-30) cc_final: 0.8980 (m-30) REVERT: C 72 MET cc_start: 0.9074 (tpt) cc_final: 0.8596 (tpt) REVERT: C 101 LEU cc_start: 0.8862 (tp) cc_final: 0.8550 (tp) REVERT: C 179 MET cc_start: 0.8995 (tpp) cc_final: 0.8609 (mmm) REVERT: C 243 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8778 (mpp) REVERT: C 282 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9104 (mm-40) REVERT: D 34 MET cc_start: 0.8338 (tpp) cc_final: 0.7898 (tpp) REVERT: D 72 MET cc_start: 0.9128 (tpt) cc_final: 0.8669 (tpp) REVERT: D 101 LEU cc_start: 0.8980 (tp) cc_final: 0.8696 (tp) REVERT: D 105 MET cc_start: 0.8775 (mmt) cc_final: 0.8363 (mmt) REVERT: D 171 GLN cc_start: 0.9009 (pt0) cc_final: 0.8702 (pm20) REVERT: D 235 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (mm110) REVERT: D 255 TRP cc_start: 0.8857 (m-10) cc_final: 0.8464 (m-10) REVERT: E 34 MET cc_start: 0.7851 (tpp) cc_final: 0.7544 (tpp) REVERT: E 152 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8781 (mm) REVERT: E 255 TRP cc_start: 0.8957 (m-10) cc_final: 0.8630 (m-90) REVERT: E 300 ASP cc_start: 0.9312 (m-30) cc_final: 0.8976 (m-30) REVERT: E 353 PHE cc_start: 0.9240 (t80) cc_final: 0.9001 (t80) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 0.2143 time to fit residues: 57.4449 Evaluate side-chains 166 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 170 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 B residue 243 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 192 VAL 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 100 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 235 GLN 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 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 154 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 166 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 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 = 0.2846 r_free = 0.2846 target = 0.039558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031449 restraints weight = 94784.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.032587 restraints weight = 54503.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.033432 restraints weight = 36667.652| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14255 Z= 0.128 Angle : 0.773 14.260 19470 Z= 0.367 Chirality : 0.044 0.267 2300 Planarity : 0.004 0.039 2360 Dihedral : 7.658 59.798 2745 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.83 % Allowed : 18.73 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1700 helix: 1.49 (0.22), residues: 575 sheet: 0.28 (0.26), residues: 400 loop : -0.47 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 255 HIS 0.003 0.001 HIS A 125 PHE 0.024 0.001 PHE D 353 TYR 0.018 0.001 TYR A 144 ARG 0.007 0.000 ARG E 75 Details of bonding type rmsd link_BETA1-4 : bond 0.00746 ( 5) link_BETA1-4 : angle 1.18875 ( 15) hydrogen bonds : bond 0.03701 ( 691) hydrogen bonds : angle 4.81640 ( 2418) SS BOND : bond 0.00091 ( 5) SS BOND : angle 0.37787 ( 10) covalent geometry : bond 0.00286 (14245) covalent geometry : angle 0.77323 (19445) *********************** 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 178 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8470 (tpp) cc_final: 0.8065 (tpp) REVERT: A 82 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8750 (mp10) REVERT: A 126 GLU cc_start: 0.8888 (mp0) cc_final: 0.8520 (tp30) REVERT: A 249 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9319 (mp) REVERT: A 282 GLN cc_start: 0.9320 (mm-40) cc_final: 0.8986 (mm-40) REVERT: B 72 MET cc_start: 0.9034 (tpp) cc_final: 0.8505 (tpp) REVERT: B 101 LEU cc_start: 0.8698 (tp) cc_final: 0.8309 (tp) REVERT: B 105 MET cc_start: 0.8778 (mmt) cc_final: 0.8407 (mmt) REVERT: B 156 MET cc_start: 0.8512 (mtp) cc_final: 0.8133 (mtt) REVERT: B 163 MET cc_start: 0.8591 (pmm) cc_final: 0.8327 (mpp) REVERT: B 179 MET cc_start: 0.9025 (tpp) cc_final: 0.8586 (mmm) REVERT: B 244 TYR cc_start: 0.9138 (m-80) cc_final: 0.8807 (m-80) REVERT: B 292 LYS cc_start: 0.8979 (mttt) cc_final: 0.8651 (mtmm) REVERT: B 300 ASP cc_start: 0.9331 (m-30) cc_final: 0.9001 (m-30) REVERT: C 72 MET cc_start: 0.9027 (tpt) cc_final: 0.8555 (tpt) REVERT: C 101 LEU cc_start: 0.8861 (tp) cc_final: 0.8532 (tp) REVERT: C 179 MET cc_start: 0.8971 (tpp) cc_final: 0.8625 (mmm) REVERT: C 243 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8701 (mpp) REVERT: C 282 GLN cc_start: 0.9458 (mm-40) cc_final: 0.9049 (mm-40) REVERT: C 300 ASP cc_start: 0.9255 (m-30) cc_final: 0.8869 (m-30) REVERT: D 34 MET cc_start: 0.8297 (tpp) cc_final: 0.7841 (tpp) REVERT: D 72 MET cc_start: 0.9097 (tpt) cc_final: 0.8625 (tpp) REVERT: D 75 ARG cc_start: 0.9060 (ttm110) cc_final: 0.8767 (ttm-80) REVERT: D 101 LEU cc_start: 0.9007 (tp) cc_final: 0.8708 (tp) REVERT: D 105 MET cc_start: 0.8722 (mmt) cc_final: 0.8350 (mmt) REVERT: D 171 GLN cc_start: 0.9020 (pt0) cc_final: 0.8675 (pm20) REVERT: D 243 MET cc_start: 0.9076 (mmm) cc_final: 0.8841 (mmp) REVERT: D 255 TRP cc_start: 0.8815 (m-10) cc_final: 0.8425 (m-10) REVERT: E 34 MET cc_start: 0.7876 (tpp) cc_final: 0.7650 (tpp) REVERT: E 152 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8825 (mm) REVERT: E 179 MET cc_start: 0.9005 (tpp) cc_final: 0.8524 (mmp) REVERT: E 255 TRP cc_start: 0.8878 (m-10) cc_final: 0.8546 (m-90) REVERT: E 279 MET cc_start: 0.9194 (tpt) cc_final: 0.8960 (tpp) REVERT: E 300 ASP cc_start: 0.9306 (m-30) cc_final: 0.8926 (m-30) REVERT: E 353 PHE cc_start: 0.9227 (t80) cc_final: 0.9000 (t80) outliers start: 26 outliers final: 15 residues processed: 165 average time/residue: 0.2204 time to fit residues: 56.6897 Evaluate side-chains 164 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 353 PHE 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 100 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 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 = 0.2847 r_free = 0.2847 target = 0.039707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.031500 restraints weight = 94745.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.032655 restraints weight = 54175.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033491 restraints weight = 36473.186| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14255 Z= 0.128 Angle : 0.790 17.367 19470 Z= 0.370 Chirality : 0.044 0.309 2300 Planarity : 0.004 0.057 2360 Dihedral : 7.512 59.495 2745 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.55 % Allowed : 18.52 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1700 helix: 1.40 (0.22), residues: 575 sheet: 0.28 (0.26), residues: 400 loop : -0.50 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 255 HIS 0.003 0.001 HIS A 125 PHE 0.022 0.001 PHE D 353 TYR 0.017 0.001 TYR E 144 ARG 0.015 0.000 ARG E 75 Details of bonding type rmsd link_BETA1-4 : bond 0.00801 ( 5) link_BETA1-4 : angle 1.16889 ( 15) hydrogen bonds : bond 0.03612 ( 691) hydrogen bonds : angle 4.75845 ( 2418) SS BOND : bond 0.00054 ( 5) SS BOND : angle 0.39488 ( 10) covalent geometry : bond 0.00294 (14245) covalent geometry : angle 0.78941 (19445) ********************** 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 178 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8458 (tpp) cc_final: 0.8053 (tpp) REVERT: A 72 MET cc_start: 0.8921 (tpp) cc_final: 0.8368 (tpp) REVERT: A 126 GLU cc_start: 0.8909 (mp0) cc_final: 0.8536 (tp30) REVERT: A 249 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9419 (mm) REVERT: A 282 GLN cc_start: 0.9339 (mm-40) cc_final: 0.8977 (mm-40) REVERT: B 72 MET cc_start: 0.9056 (tpp) cc_final: 0.8520 (tpp) REVERT: B 101 LEU cc_start: 0.8669 (tp) cc_final: 0.8271 (tp) REVERT: B 105 MET cc_start: 0.8822 (mmt) cc_final: 0.8532 (mmt) REVERT: B 156 MET cc_start: 0.8575 (mtp) cc_final: 0.8214 (mtt) REVERT: B 163 MET cc_start: 0.8597 (pmm) cc_final: 0.8395 (mpp) REVERT: B 179 MET cc_start: 0.9044 (tpp) cc_final: 0.8635 (mmm) REVERT: B 244 TYR cc_start: 0.9147 (m-80) cc_final: 0.8831 (m-80) REVERT: B 292 LYS cc_start: 0.8983 (mttt) cc_final: 0.8650 (mtmm) REVERT: B 300 ASP cc_start: 0.9337 (m-30) cc_final: 0.9008 (m-30) REVERT: C 72 MET cc_start: 0.9025 (tpt) cc_final: 0.8558 (tpt) REVERT: C 101 LEU cc_start: 0.8877 (tp) cc_final: 0.8553 (tp) REVERT: C 179 MET cc_start: 0.8948 (tpp) cc_final: 0.8632 (mmm) REVERT: C 243 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8750 (mpp) REVERT: C 282 GLN cc_start: 0.9467 (mm-40) cc_final: 0.9059 (mm-40) REVERT: C 300 ASP cc_start: 0.9252 (m-30) cc_final: 0.8869 (m-30) REVERT: D 34 MET cc_start: 0.8335 (tpp) cc_final: 0.7862 (tpp) REVERT: D 72 MET cc_start: 0.9094 (tpt) cc_final: 0.8639 (tpp) REVERT: D 101 LEU cc_start: 0.9058 (tp) cc_final: 0.8727 (tp) REVERT: D 105 MET cc_start: 0.8713 (mmt) cc_final: 0.8458 (mmt) REVERT: D 163 MET cc_start: 0.8827 (mpp) cc_final: 0.8591 (mmm) REVERT: D 171 GLN cc_start: 0.9048 (pt0) cc_final: 0.8689 (pm20) REVERT: D 255 TRP cc_start: 0.8771 (m-10) cc_final: 0.8416 (m-10) REVERT: D 303 MET cc_start: 0.9326 (mmm) cc_final: 0.8981 (mmm) REVERT: E 34 MET cc_start: 0.7908 (tpp) cc_final: 0.7698 (tpp) REVERT: E 72 MET cc_start: 0.8867 (tpp) cc_final: 0.8281 (tpp) REVERT: E 255 TRP cc_start: 0.8837 (m-10) cc_final: 0.8537 (m-90) REVERT: E 279 MET cc_start: 0.9186 (tpt) cc_final: 0.8962 (tpp) REVERT: E 300 ASP cc_start: 0.9311 (m-30) cc_final: 0.8930 (m-30) REVERT: E 353 PHE cc_start: 0.9218 (t80) cc_final: 0.8969 (t80) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.2168 time to fit residues: 57.1951 Evaluate side-chains 162 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 353 PHE 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 100 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 133 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 44 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 70 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 127 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.031453 restraints weight = 95785.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.032586 restraints weight = 55376.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.033409 restraints weight = 37424.781| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14255 Z= 0.135 Angle : 0.782 15.113 19470 Z= 0.368 Chirality : 0.044 0.308 2300 Planarity : 0.004 0.049 2360 Dihedral : 7.436 59.563 2745 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.48 % Allowed : 18.73 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1700 helix: 1.45 (0.22), residues: 575 sheet: 0.26 (0.26), residues: 400 loop : -0.47 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 255 HIS 0.005 0.001 HIS B 125 PHE 0.020 0.001 PHE D 353 TYR 0.016 0.001 TYR E 144 ARG 0.013 0.000 ARG E 75 Details of bonding type rmsd link_BETA1-4 : bond 0.00723 ( 5) link_BETA1-4 : angle 1.30554 ( 15) hydrogen bonds : bond 0.03565 ( 691) hydrogen bonds : angle 4.73874 ( 2418) SS BOND : bond 0.00049 ( 5) SS BOND : angle 0.37528 ( 10) covalent geometry : bond 0.00310 (14245) covalent geometry : angle 0.78139 (19445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.83 seconds wall clock time: 72 minutes 22.76 seconds (4342.76 seconds total)