Starting phenix.real_space_refine on Fri Mar 6 02:15:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774.map" model { file = "/net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zl1_14774/03_2026/7zl1_14774_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 8448 2.51 5 N 2272 2.21 5 O 2883 1.98 5 H 13574 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27257 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "D" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "E" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "H" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "G" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "F" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 138 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 144 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "E" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 138 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 135 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "G" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 141 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 5.02, per 1000 atoms: 0.18 Number of scatterers: 27257 At special positions: 0 Unit cell: (101.156, 99.484, 99.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2883 8.00 N 2272 7.00 C 8448 6.00 H 13574 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.04 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS G 317 " distance=2.04 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 357 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS H 318 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS H 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 357 " distance=2.04 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 317 " - pdb=" SG CYS E 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS E 317 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS F 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS F 317 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 357 " distance=2.04 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 357 " distance=2.04 Simple disulfide: pdb=" SG CYS H 210 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.04 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 357 " distance=2.04 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 271 " 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 NAG-ASN " NAG A1000 " - " ASN A 220 " " NAG B1000 " - " ASN B 220 " " NAG C1000 " - " ASN C 220 " " NAG D1000 " - " ASN D 220 " " NAG E1000 " - " ASN E 220 " " NAG F1000 " - " ASN F 220 " " NAG G1000 " - " ASN G 220 " " NAG H1000 " - " ASN H 220 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 856.7 milliseconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 16 sheets defined 13.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.525A pdb=" N GLY B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 removed outlier: 4.199A pdb=" N HIS B 358 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.550A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 4.464A pdb=" N HIS A 358 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.588A pdb=" N GLY D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 359 removed outlier: 4.325A pdb=" N HIS D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.588A pdb=" N GLY C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 4.325A pdb=" N HIS C 358 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 removed outlier: 3.751A pdb=" N SER E 173 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.641A pdb=" N GLY E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 removed outlier: 3.890A pdb=" N HIS E 358 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 173 Processing helix chain 'H' and resid 277 through 279 No H-bonds generated for 'chain 'H' and resid 277 through 279' Processing helix chain 'H' and resid 324 through 328 Processing helix chain 'H' and resid 344 through 352 removed outlier: 3.614A pdb=" N GLY H 352 " --> pdb=" O ILE H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 removed outlier: 4.430A pdb=" N HIS H 358 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 removed outlier: 3.522A pdb=" N SER G 173 " --> pdb=" O TRP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 279 No H-bonds generated for 'chain 'G' and resid 277 through 279' Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 344 through 352 Processing helix chain 'G' and resid 355 through 359 removed outlier: 4.406A pdb=" N HIS G 358 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 174 removed outlier: 3.537A pdb=" N ARG F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.591A pdb=" N GLY F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 4.347A pdb=" N HIS F 358 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 293 removed outlier: 5.406A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 285 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP B 212 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY B 335 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 214 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 333 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.252A pdb=" N LEU B 240 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 223 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 293 removed outlier: 5.357A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 285 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP A 212 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY A 335 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS A 214 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 333 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 258 removed outlier: 6.136A pdb=" N LEU A 240 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE A 223 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.539A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP D 212 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY D 335 " --> pdb=" O TRP D 212 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS D 214 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 333 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 255 through 258 removed outlier: 6.225A pdb=" N LEU D 240 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE D 223 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU D 308 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU D 370 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 288 through 293 removed outlier: 5.387A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 285 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP C 212 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY C 335 " --> pdb=" O TRP C 212 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS C 214 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU C 333 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 255 through 258 removed outlier: 6.215A pdb=" N LEU C 240 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 223 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 308 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU C 370 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 288 through 293 removed outlier: 6.682A pdb=" N LEU E 283 " --> pdb=" O ALA E 290 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR E 292 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR E 281 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP E 212 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY E 335 " --> pdb=" O TRP E 212 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS E 214 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 333 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 255 through 258 removed outlier: 6.268A pdb=" N LEU E 240 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE E 223 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU E 308 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU E 370 " --> pdb=" O HIS E 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 288 through 293 removed outlier: 5.336A pdb=" N LEU H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL H 285 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP H 212 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY H 335 " --> pdb=" O TRP H 212 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS H 214 " --> pdb=" O LEU H 333 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU H 333 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 255 through 258 removed outlier: 6.246A pdb=" N LEU H 240 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE H 223 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU H 308 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU H 370 " --> pdb=" O HIS H 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 288 through 293 removed outlier: 5.339A pdb=" N LEU G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL G 285 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP G 212 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY G 335 " --> pdb=" O TRP G 212 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS G 214 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU G 333 " --> pdb=" O LYS G 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 255 through 258 removed outlier: 6.195A pdb=" N LEU G 240 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE G 223 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU G 370 " --> pdb=" O HIS G 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 288 through 293 removed outlier: 5.339A pdb=" N LEU F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL F 285 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP F 212 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLY F 335 " --> pdb=" O TRP F 212 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS F 214 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU F 333 " --> pdb=" O LYS F 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 255 through 258 removed outlier: 6.218A pdb=" N LEU F 240 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE F 223 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU F 308 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU F 370 " --> pdb=" O HIS F 197 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1248 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: 7.37 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13574 1.04 - 1.25: 2109 1.25 - 1.46: 4595 1.46 - 1.66: 6808 1.66 - 1.87: 112 Bond restraints: 27198 Sorted by residual: bond pdb=" CA LYS B 214 " pdb=" CB LYS B 214 " ideal model delta sigma weight residual 1.539 1.436 0.103 4.88e-02 4.20e+02 4.47e+00 bond pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" C1 NAG D1000 " pdb=" C2 NAG D1000 " ideal model delta sigma weight residual 1.532 1.568 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" CA LYS F 214 " pdb=" CB LYS F 214 " ideal model delta sigma weight residual 1.539 1.451 0.088 4.88e-02 4.20e+02 3.27e+00 bond pdb=" N GLN F 167 " pdb=" CA GLN F 167 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 ... (remaining 27193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 44821 1.44 - 2.89: 2594 2.89 - 4.33: 484 4.33 - 5.78: 51 5.78 - 7.22: 13 Bond angle restraints: 47963 Sorted by residual: angle pdb=" N LYS D 314 " pdb=" CA LYS D 314 " pdb=" C LYS D 314 " ideal model delta sigma weight residual 111.33 115.88 -4.55 1.21e+00 6.83e-01 1.41e+01 angle pdb=" N MET F 261 " pdb=" CA MET F 261 " pdb=" C MET F 261 " ideal model delta sigma weight residual 110.41 114.81 -4.40 1.18e+00 7.18e-01 1.39e+01 angle pdb=" C LEU C 270 " pdb=" N CYS C 271 " pdb=" CA CYS C 271 " ideal model delta sigma weight residual 121.89 115.52 6.37 1.74e+00 3.30e-01 1.34e+01 angle pdb=" C LEU E 270 " pdb=" N CYS E 271 " pdb=" CA CYS E 271 " ideal model delta sigma weight residual 121.86 116.16 5.70 1.58e+00 4.01e-01 1.30e+01 angle pdb=" C LEU H 270 " pdb=" N CYS H 271 " pdb=" CA CYS H 271 " ideal model delta sigma weight residual 121.86 116.20 5.66 1.58e+00 4.01e-01 1.28e+01 ... (remaining 47958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10919 17.99 - 35.97: 996 35.97 - 53.96: 372 53.96 - 71.95: 253 71.95 - 89.93: 28 Dihedral angle restraints: 12568 sinusoidal: 6816 harmonic: 5752 Sorted by residual: dihedral pdb=" CB CYS D 317 " pdb=" SG CYS D 317 " pdb=" SG CYS E 318 " pdb=" CB CYS E 318 " ideal model delta sinusoidal sigma weight residual 93.00 170.56 -77.56 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS F 317 " pdb=" CB CYS F 317 " ideal model delta sinusoidal sigma weight residual -86.00 -144.44 58.44 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS H 210 " pdb=" SG CYS H 210 " pdb=" SG CYS H 271 " pdb=" CB CYS H 271 " ideal model delta sinusoidal sigma weight residual -86.00 -33.05 -52.95 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 12565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1195 0.042 - 0.085: 597 0.085 - 0.127: 193 0.127 - 0.169: 44 0.169 - 0.212: 11 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO B 176 " pdb=" N PRO B 176 " pdb=" C PRO B 176 " pdb=" CB PRO B 176 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO F 176 " pdb=" N PRO F 176 " pdb=" C PRO F 176 " pdb=" CB PRO F 176 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1 NAG F1000 " pdb=" ND2 ASN F 220 " pdb=" C2 NAG F1000 " pdb=" O5 NAG F1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 2037 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 266 " -0.322 9.50e-02 1.11e+02 1.11e-01 2.91e+01 pdb=" NE ARG F 266 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG F 266 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG F 266 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 266 " 0.056 2.00e-02 2.50e+03 pdb="HH11 ARG F 266 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG F 266 " -0.003 2.00e-02 2.50e+03 pdb="HH21 ARG F 266 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 266 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 267 " 0.023 2.00e-02 2.50e+03 2.58e-02 2.67e+01 pdb=" CG TRP B 267 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 267 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 267 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 267 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 267 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 267 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 267 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 267 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 267 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP B 267 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 267 " 0.066 2.00e-02 2.50e+03 pdb=" HE3 TRP B 267 " -0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 267 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 267 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP B 267 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 267 " 0.019 2.00e-02 2.50e+03 2.29e-02 2.10e+01 pdb=" CG TRP F 267 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP F 267 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP F 267 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 267 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP F 267 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 267 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 267 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 267 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 267 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP F 267 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP F 267 " 0.058 2.00e-02 2.50e+03 pdb=" HE3 TRP F 267 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 267 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 267 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP F 267 " 0.005 2.00e-02 2.50e+03 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 896 2.10 - 2.72: 46035 2.72 - 3.35: 80619 3.35 - 3.97: 116145 3.97 - 4.60: 175889 Nonbonded interactions: 419584 Sorted by model distance: nonbonded pdb=" O PRO B 176 " pdb=" H1 HOH B1101 " model vdw 1.469 2.450 nonbonded pdb=" O PRO A 176 " pdb=" H1 HOH A1101 " model vdw 1.483 2.450 nonbonded pdb=" O GLY A 375 " pdb=" H1 HOH A1102 " model vdw 1.484 2.450 nonbonded pdb=" O GLY C 375 " pdb=" H1 HOH C1102 " model vdw 1.485 2.450 nonbonded pdb=" O GLY D 375 " pdb=" H1 HOH D1103 " model vdw 1.501 2.450 ... (remaining 419579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 4.300 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: 0.180 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.870 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 13656 Z= 0.302 Angle : 0.902 8.670 18568 Z= 0.502 Chirality : 0.056 0.212 2040 Planarity : 0.010 0.115 2352 Dihedral : 14.805 89.932 4896 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 5.69 % Favored : 93.31 % Rotamer: Outliers : 0.65 % Allowed : 3.66 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1704 helix: -2.00 (0.30), residues: 136 sheet: 1.04 (0.22), residues: 512 loop : -0.24 (0.22), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.004 ARG D 172 TYR 0.035 0.006 TYR G 239 PHE 0.033 0.004 PHE E 247 TRP 0.036 0.004 TRP B 267 HIS 0.013 0.003 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00690 (13624) covalent geometry : angle 0.87959 (18496) SS BOND : bond 0.00977 ( 24) SS BOND : angle 2.90589 ( 48) hydrogen bonds : bond 0.15727 ( 514) hydrogen bonds : angle 7.56884 ( 1248) link_NAG-ASN : bond 0.01222 ( 8) link_NAG-ASN : angle 4.03289 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.607 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: B 254 ASN cc_start: 0.8180 (m110) cc_final: 0.7898 (m110) REVERT: A 255 LYS cc_start: 0.8268 (mttm) cc_final: 0.7997 (mtmm) REVERT: A 288 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7088 (mt-10) REVERT: D 288 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7103 (mt-10) REVERT: C 203 ARG cc_start: 0.7793 (ttt-90) cc_final: 0.7546 (ttt-90) REVERT: E 203 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7614 (ttt-90) REVERT: E 254 ASN cc_start: 0.8059 (m110) cc_final: 0.7666 (m110) REVERT: H 203 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7585 (ttt-90) REVERT: G 203 ARG cc_start: 0.7810 (ttt-90) cc_final: 0.7572 (ttt-90) REVERT: G 254 ASN cc_start: 0.8053 (m110) cc_final: 0.7853 (m110) REVERT: G 255 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7950 (mtpt) REVERT: F 172 ARG cc_start: 0.6859 (ptt-90) cc_final: 0.6618 (ptm-80) REVERT: F 173 SER cc_start: 0.7910 (t) cc_final: 0.7678 (p) REVERT: F 203 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7566 (ttt-90) REVERT: F 231 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7445 (mtt180) outliers start: 9 outliers final: 8 residues processed: 205 average time/residue: 1.8619 time to fit residues: 406.7814 Evaluate side-chains 167 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain F residue 187 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 ASN C 345 ASN H 345 ASN F 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105017 restraints weight = 40250.019| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.84 r_work: 0.3059 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13656 Z= 0.171 Angle : 0.664 7.247 18568 Z= 0.362 Chirality : 0.048 0.137 2040 Planarity : 0.004 0.035 2352 Dihedral : 8.262 59.354 2016 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Rotamer: Outliers : 2.16 % Allowed : 6.97 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1704 helix: -1.75 (0.34), residues: 136 sheet: 0.74 (0.21), residues: 568 loop : -0.21 (0.23), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 266 TYR 0.014 0.002 TYR A 239 PHE 0.015 0.002 PHE H 323 TRP 0.013 0.002 TRP C 284 HIS 0.005 0.002 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00381 (13624) covalent geometry : angle 0.64743 (18496) SS BOND : bond 0.01001 ( 24) SS BOND : angle 2.38490 ( 48) hydrogen bonds : bond 0.04616 ( 514) hydrogen bonds : angle 6.10277 ( 1248) link_NAG-ASN : bond 0.00651 ( 8) link_NAG-ASN : angle 2.62070 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.569 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: B 203 ARG cc_start: 0.7933 (ttt-90) cc_final: 0.7277 (ttt90) REVERT: B 254 ASN cc_start: 0.8057 (m110) cc_final: 0.7729 (m110) REVERT: A 172 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6365 (ptp90) REVERT: A 255 LYS cc_start: 0.8185 (mttm) cc_final: 0.7842 (mttt) REVERT: D 254 ASN cc_start: 0.8132 (m110) cc_final: 0.7829 (m110) REVERT: C 254 ASN cc_start: 0.8097 (m110) cc_final: 0.7828 (m110) REVERT: C 355 GLU cc_start: 0.7391 (tp30) cc_final: 0.7174 (tp30) REVERT: G 255 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7948 (mtpt) REVERT: F 172 ARG cc_start: 0.6799 (ptt-90) cc_final: 0.6359 (ptm-80) REVERT: F 173 SER cc_start: 0.7914 (t) cc_final: 0.7464 (p) REVERT: F 231 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7460 (mmt-90) REVERT: F 243 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5782 (pp30) outliers start: 30 outliers final: 15 residues processed: 188 average time/residue: 1.8548 time to fit residues: 372.3482 Evaluate side-chains 169 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 355 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN E 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103794 restraints weight = 40111.921| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.82 r_work: 0.3049 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13656 Z= 0.200 Angle : 0.677 12.012 18568 Z= 0.366 Chirality : 0.048 0.154 2040 Planarity : 0.004 0.053 2352 Dihedral : 7.836 58.564 2016 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 2.51 % Allowed : 8.12 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1704 helix: -1.28 (0.41), residues: 120 sheet: 0.84 (0.21), residues: 528 loop : -0.42 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 266 TYR 0.015 0.002 TYR A 239 PHE 0.014 0.002 PHE C 323 TRP 0.012 0.002 TRP C 169 HIS 0.006 0.002 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00462 (13624) covalent geometry : angle 0.65772 (18496) SS BOND : bond 0.01123 ( 24) SS BOND : angle 2.62840 ( 48) hydrogen bonds : bond 0.04585 ( 514) hydrogen bonds : angle 5.90861 ( 1248) link_NAG-ASN : bond 0.00872 ( 8) link_NAG-ASN : angle 2.62192 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.774 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: B 254 ASN cc_start: 0.7967 (m110) cc_final: 0.7634 (m110) REVERT: A 172 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6404 (ptp90) REVERT: A 255 LYS cc_start: 0.8184 (mttm) cc_final: 0.7910 (mttt) REVERT: D 254 ASN cc_start: 0.8072 (m110) cc_final: 0.7817 (m110) REVERT: D 355 GLU cc_start: 0.7527 (tp30) cc_final: 0.7280 (tp30) REVERT: C 254 ASN cc_start: 0.8103 (m110) cc_final: 0.7810 (m110) REVERT: G 231 ARG cc_start: 0.7702 (mpt180) cc_final: 0.7448 (mmt-90) REVERT: G 280 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7864 (tt) REVERT: F 172 ARG cc_start: 0.6754 (ptt-90) cc_final: 0.6516 (ptm-80) REVERT: F 173 SER cc_start: 0.8058 (t) cc_final: 0.7714 (p) REVERT: F 243 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5613 (pp30) REVERT: F 350 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: F 355 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7020 (tp30) outliers start: 35 outliers final: 22 residues processed: 187 average time/residue: 1.9074 time to fit residues: 381.5520 Evaluate side-chains 181 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 359 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104398 restraints weight = 39692.726| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.81 r_work: 0.3052 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13656 Z= 0.183 Angle : 0.637 7.955 18568 Z= 0.345 Chirality : 0.047 0.157 2040 Planarity : 0.004 0.038 2352 Dihedral : 7.540 59.587 2016 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 3.16 % Allowed : 8.76 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1704 helix: -1.17 (0.45), residues: 120 sheet: 0.83 (0.21), residues: 528 loop : -0.51 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 266 TYR 0.014 0.002 TYR B 239 PHE 0.011 0.002 PHE H 323 TRP 0.010 0.002 TRP F 339 HIS 0.005 0.002 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00421 (13624) covalent geometry : angle 0.62131 (18496) SS BOND : bond 0.00971 ( 24) SS BOND : angle 2.43026 ( 48) hydrogen bonds : bond 0.04225 ( 514) hydrogen bonds : angle 5.82871 ( 1248) link_NAG-ASN : bond 0.00867 ( 8) link_NAG-ASN : angle 2.23878 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.725 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: B 254 ASN cc_start: 0.7898 (m110) cc_final: 0.7551 (m110) REVERT: B 280 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 255 LYS cc_start: 0.8143 (mttm) cc_final: 0.7915 (mttt) REVERT: D 254 ASN cc_start: 0.8018 (m110) cc_final: 0.7755 (m110) REVERT: D 355 GLU cc_start: 0.7573 (tp30) cc_final: 0.7353 (tp30) REVERT: C 172 ARG cc_start: 0.6878 (ptm-80) cc_final: 0.6537 (ptm-80) REVERT: C 254 ASN cc_start: 0.8045 (m110) cc_final: 0.7785 (m110) REVERT: E 231 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7230 (mmt-90) REVERT: E 355 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7177 (mp0) REVERT: H 280 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7858 (tt) REVERT: G 280 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7924 (tt) REVERT: F 172 ARG cc_start: 0.6698 (ptt-90) cc_final: 0.6462 (ptm-80) REVERT: F 173 SER cc_start: 0.8027 (t) cc_final: 0.7747 (p) REVERT: F 243 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5761 (pp30) REVERT: F 355 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7103 (tp30) outliers start: 44 outliers final: 24 residues processed: 185 average time/residue: 1.9080 time to fit residues: 377.0714 Evaluate side-chains 180 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104557 restraints weight = 39805.508| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.81 r_work: 0.3059 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13656 Z= 0.177 Angle : 0.635 15.166 18568 Z= 0.341 Chirality : 0.047 0.211 2040 Planarity : 0.004 0.039 2352 Dihedral : 7.416 59.764 2016 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 3.38 % Allowed : 9.05 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1704 helix: -1.12 (0.46), residues: 120 sheet: 0.55 (0.20), residues: 616 loop : -0.60 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 266 TYR 0.014 0.002 TYR B 239 PHE 0.009 0.002 PHE H 323 TRP 0.010 0.002 TRP A 284 HIS 0.006 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00410 (13624) covalent geometry : angle 0.61683 (18496) SS BOND : bond 0.00896 ( 24) SS BOND : angle 2.58054 ( 48) hydrogen bonds : bond 0.04099 ( 514) hydrogen bonds : angle 5.78410 ( 1248) link_NAG-ASN : bond 0.00780 ( 8) link_NAG-ASN : angle 2.24443 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.583 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: B 280 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 243 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5737 (pp30) REVERT: A 255 LYS cc_start: 0.8117 (mttm) cc_final: 0.7852 (mtmm) REVERT: A 280 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 355 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: D 355 GLU cc_start: 0.7591 (tp30) cc_final: 0.7327 (tp30) REVERT: C 172 ARG cc_start: 0.6858 (ptm-80) cc_final: 0.6532 (ptm-80) REVERT: C 254 ASN cc_start: 0.8028 (m110) cc_final: 0.7753 (m110) REVERT: E 231 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7234 (mmt-90) REVERT: E 280 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7878 (tt) REVERT: E 355 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7149 (mp0) REVERT: H 280 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (tt) REVERT: G 280 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7939 (tt) REVERT: F 172 ARG cc_start: 0.6650 (ptt-90) cc_final: 0.6400 (ptm-80) REVERT: F 173 SER cc_start: 0.8073 (t) cc_final: 0.7778 (p) REVERT: F 243 GLN cc_start: 0.6036 (OUTLIER) cc_final: 0.5815 (pp30) REVERT: F 355 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7086 (tp30) outliers start: 47 outliers final: 27 residues processed: 181 average time/residue: 1.7270 time to fit residues: 334.9141 Evaluate side-chains 183 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104986 restraints weight = 39933.681| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.81 r_work: 0.3065 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 13656 Z= 0.170 Angle : 0.624 15.015 18568 Z= 0.334 Chirality : 0.047 0.187 2040 Planarity : 0.004 0.042 2352 Dihedral : 7.276 59.831 2016 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 3.74 % Allowed : 9.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1704 helix: -1.06 (0.47), residues: 120 sheet: 0.53 (0.20), residues: 616 loop : -0.67 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 266 TYR 0.014 0.002 TYR B 239 PHE 0.009 0.002 PHE E 225 TRP 0.009 0.002 TRP B 339 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00397 (13624) covalent geometry : angle 0.60606 (18496) SS BOND : bond 0.00877 ( 24) SS BOND : angle 2.56587 ( 48) hydrogen bonds : bond 0.03990 ( 514) hydrogen bonds : angle 5.71121 ( 1248) link_NAG-ASN : bond 0.00775 ( 8) link_NAG-ASN : angle 2.19816 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.786 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: B 280 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (tt) REVERT: B 343 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 255 LYS cc_start: 0.8064 (mttm) cc_final: 0.7798 (mtmm) REVERT: A 280 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7915 (tt) REVERT: D 355 GLU cc_start: 0.7557 (tp30) cc_final: 0.7303 (tp30) REVERT: C 172 ARG cc_start: 0.6929 (ptm-80) cc_final: 0.6584 (ptm-80) REVERT: E 280 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7895 (tt) REVERT: G 280 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7938 (tt) REVERT: F 172 ARG cc_start: 0.6627 (ptt-90) cc_final: 0.6357 (ptm-80) REVERT: F 173 SER cc_start: 0.8081 (t) cc_final: 0.7794 (p) REVERT: F 243 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5941 (pp30) REVERT: F 355 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7106 (tp30) outliers start: 52 outliers final: 27 residues processed: 176 average time/residue: 1.7021 time to fit residues: 321.7969 Evaluate side-chains 177 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104879 restraints weight = 39598.713| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.80 r_work: 0.3066 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13656 Z= 0.174 Angle : 0.631 15.435 18568 Z= 0.337 Chirality : 0.047 0.191 2040 Planarity : 0.004 0.039 2352 Dihedral : 7.278 59.864 2016 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.45 % Allowed : 9.41 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1704 helix: -1.03 (0.47), residues: 120 sheet: 0.53 (0.20), residues: 616 loop : -0.72 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 231 TYR 0.014 0.002 TYR F 239 PHE 0.009 0.002 PHE E 225 TRP 0.009 0.002 TRP F 339 HIS 0.006 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00405 (13624) covalent geometry : angle 0.61298 (18496) SS BOND : bond 0.00833 ( 24) SS BOND : angle 2.58465 ( 48) hydrogen bonds : bond 0.04019 ( 514) hydrogen bonds : angle 5.68354 ( 1248) link_NAG-ASN : bond 0.00754 ( 8) link_NAG-ASN : angle 2.26909 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.532 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: B 280 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7926 (tt) REVERT: B 343 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 243 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5898 (pp30) REVERT: A 255 LYS cc_start: 0.8066 (mttm) cc_final: 0.7799 (mtmm) REVERT: D 355 GLU cc_start: 0.7527 (tp30) cc_final: 0.7287 (tp30) REVERT: E 231 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.7280 (mmt-90) REVERT: E 280 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (tt) REVERT: G 280 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7974 (tt) REVERT: F 172 ARG cc_start: 0.6641 (ptt-90) cc_final: 0.6320 (ptm-80) REVERT: F 173 SER cc_start: 0.8104 (t) cc_final: 0.7831 (p) REVERT: F 243 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5978 (pp30) REVERT: F 355 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7097 (tp30) outliers start: 48 outliers final: 29 residues processed: 174 average time/residue: 1.6960 time to fit residues: 317.4325 Evaluate side-chains 176 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104811 restraints weight = 39737.365| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.80 r_work: 0.3064 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13656 Z= 0.182 Angle : 0.642 15.358 18568 Z= 0.343 Chirality : 0.047 0.192 2040 Planarity : 0.004 0.038 2352 Dihedral : 7.293 59.982 2016 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 3.52 % Allowed : 9.63 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1704 helix: -1.04 (0.47), residues: 120 sheet: 0.51 (0.20), residues: 616 loop : -0.78 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 231 TYR 0.014 0.002 TYR F 239 PHE 0.009 0.002 PHE A 225 TRP 0.009 0.002 TRP B 339 HIS 0.005 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00423 (13624) covalent geometry : angle 0.62360 (18496) SS BOND : bond 0.00841 ( 24) SS BOND : angle 2.64484 ( 48) hydrogen bonds : bond 0.04059 ( 514) hydrogen bonds : angle 5.69584 ( 1248) link_NAG-ASN : bond 0.00756 ( 8) link_NAG-ASN : angle 2.32654 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.661 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: B 343 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7811 (mp) REVERT: A 255 LYS cc_start: 0.8032 (mttm) cc_final: 0.7811 (mtmm) REVERT: D 355 GLU cc_start: 0.7533 (tp30) cc_final: 0.7293 (tp30) REVERT: E 231 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.7282 (mmt-90) REVERT: E 280 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7912 (tt) REVERT: G 280 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7978 (tt) REVERT: F 173 SER cc_start: 0.8094 (t) cc_final: 0.7819 (p) REVERT: F 243 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5890 (pp30) REVERT: F 315 ASN cc_start: 0.5754 (m-40) cc_final: 0.5435 (m-40) outliers start: 49 outliers final: 28 residues processed: 174 average time/residue: 1.6232 time to fit residues: 303.9851 Evaluate side-chains 180 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105899 restraints weight = 39884.969| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.80 r_work: 0.3082 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13656 Z= 0.149 Angle : 0.627 17.146 18568 Z= 0.332 Chirality : 0.046 0.209 2040 Planarity : 0.003 0.031 2352 Dihedral : 7.086 59.901 2016 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.73 % Allowed : 10.42 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1704 helix: -1.06 (0.46), residues: 128 sheet: 0.51 (0.20), residues: 616 loop : -0.80 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 188 TYR 0.013 0.002 TYR B 239 PHE 0.010 0.001 PHE A 225 TRP 0.009 0.001 TRP G 169 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00356 (13624) covalent geometry : angle 0.60728 (18496) SS BOND : bond 0.00877 ( 24) SS BOND : angle 2.77166 ( 48) hydrogen bonds : bond 0.03738 ( 514) hydrogen bonds : angle 5.64092 ( 1248) link_NAG-ASN : bond 0.00659 ( 8) link_NAG-ASN : angle 2.16956 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.682 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: B 343 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 255 LYS cc_start: 0.8027 (mttm) cc_final: 0.7793 (mtmm) REVERT: D 355 GLU cc_start: 0.7519 (tp30) cc_final: 0.7296 (tp30) REVERT: E 231 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.7267 (mmt-90) REVERT: F 173 SER cc_start: 0.8123 (t) cc_final: 0.7877 (p) REVERT: F 243 GLN cc_start: 0.6195 (OUTLIER) cc_final: 0.5949 (pp30) REVERT: F 255 LYS cc_start: 0.8157 (mttp) cc_final: 0.7888 (mtmm) REVERT: F 315 ASN cc_start: 0.5681 (m-40) cc_final: 0.5339 (m-40) outliers start: 38 outliers final: 24 residues processed: 169 average time/residue: 1.7771 time to fit residues: 322.5236 Evaluate side-chains 170 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 0.0670 chunk 84 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107139 restraints weight = 39909.982| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.79 r_work: 0.3106 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13656 Z= 0.124 Angle : 0.598 17.416 18568 Z= 0.316 Chirality : 0.046 0.191 2040 Planarity : 0.003 0.031 2352 Dihedral : 6.738 59.382 2016 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.60 % Rotamer: Outliers : 2.30 % Allowed : 10.92 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1704 helix: -0.70 (0.49), residues: 120 sheet: 0.52 (0.20), residues: 616 loop : -0.86 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 266 TYR 0.012 0.001 TYR B 239 PHE 0.011 0.001 PHE A 225 TRP 0.009 0.001 TRP G 169 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00299 (13624) covalent geometry : angle 0.57870 (18496) SS BOND : bond 0.00787 ( 24) SS BOND : angle 2.72513 ( 48) hydrogen bonds : bond 0.03408 ( 514) hydrogen bonds : angle 5.48046 ( 1248) link_NAG-ASN : bond 0.00581 ( 8) link_NAG-ASN : angle 1.95015 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.718 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: E 231 ARG cc_start: 0.7472 (mmt-90) cc_final: 0.7213 (mmt-90) REVERT: E 261 MET cc_start: 0.6696 (mmt) cc_final: 0.5824 (mmt) REVERT: F 173 SER cc_start: 0.8116 (t) cc_final: 0.7874 (p) REVERT: F 255 LYS cc_start: 0.8122 (mttp) cc_final: 0.7874 (mtmm) outliers start: 32 outliers final: 20 residues processed: 165 average time/residue: 1.7123 time to fit residues: 303.2863 Evaluate side-chains 160 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106677 restraints weight = 39876.768| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.80 r_work: 0.3094 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13656 Z= 0.136 Angle : 0.611 16.545 18568 Z= 0.323 Chirality : 0.046 0.195 2040 Planarity : 0.003 0.031 2352 Dihedral : 6.797 59.641 2016 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.08 % Rotamer: Outliers : 2.01 % Allowed : 11.57 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1704 helix: -0.72 (0.49), residues: 120 sheet: 0.50 (0.20), residues: 616 loop : -0.86 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 266 TYR 0.012 0.002 TYR B 239 PHE 0.010 0.001 PHE A 225 TRP 0.008 0.001 TRP B 284 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00328 (13624) covalent geometry : angle 0.59158 (18496) SS BOND : bond 0.00805 ( 24) SS BOND : angle 2.73013 ( 48) hydrogen bonds : bond 0.03542 ( 514) hydrogen bonds : angle 5.46841 ( 1248) link_NAG-ASN : bond 0.00627 ( 8) link_NAG-ASN : angle 1.94638 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9264.98 seconds wall clock time: 157 minutes 10.06 seconds (9430.06 seconds total)