Starting phenix.real_space_refine on Wed Aug 27 00:38:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.map" model { file = "/net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fly_50543/08_2025/9fly_50543.cif" } resolution = 3.7 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= -0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 26901 2.51 5 N 7035 2.21 5 O 9331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43463 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "B" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "C" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "D" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "E" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "F" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Chain: "G" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6209 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 50, 'TRANS': 808} Time building chain proxies: 11.36, per 1000 atoms: 0.26 Number of scatterers: 43463 At special positions: 0 Unit cell: (102.24, 103.944, 456.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 9331 8.00 N 7035 7.00 C 26901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=70, symmetry=0 Simple disulfide: pdb=" SG CYS A4173 " - pdb=" SG CYS A4325 " distance=2.03 Simple disulfide: pdb=" SG CYS A4186 " - pdb=" SG CYS A4236 " distance=2.07 Simple disulfide: pdb=" SG CYS A4270 " - pdb=" SG CYS A4406 " distance=2.03 Simple disulfide: pdb=" SG CYS A4352 " - pdb=" SG CYS A4490 " distance=2.04 Simple disulfide: pdb=" SG CYS A4433 " - pdb=" SG CYS A4573 " distance=2.03 Simple disulfide: pdb=" SG CYS A4518 " - pdb=" SG CYS A4655 " distance=2.04 Simple disulfide: pdb=" SG CYS A4600 " - pdb=" SG CYS A4739 " distance=2.02 Simple disulfide: pdb=" SG CYS A4683 " - pdb=" SG CYS A4824 " distance=2.04 Simple disulfide: pdb=" SG CYS A4768 " - pdb=" SG CYS A4915 " distance=2.04 Simple disulfide: pdb=" SG CYS A4853 " - pdb=" SG CYS A5000 " distance=2.03 Simple disulfide: pdb=" SG CYS B4173 " - pdb=" SG CYS B4325 " distance=2.03 Simple disulfide: pdb=" SG CYS B4186 " - pdb=" SG CYS B4236 " distance=2.07 Simple disulfide: pdb=" SG CYS B4270 " - pdb=" SG CYS B4406 " distance=2.03 Simple disulfide: pdb=" SG CYS B4352 " - pdb=" SG CYS B4490 " distance=2.04 Simple disulfide: pdb=" SG CYS B4433 " - pdb=" SG CYS B4573 " distance=2.03 Simple disulfide: pdb=" SG CYS B4518 " - pdb=" SG CYS B4655 " distance=2.04 Simple disulfide: pdb=" SG CYS B4600 " - pdb=" SG CYS B4739 " distance=2.02 Simple disulfide: pdb=" SG CYS B4683 " - pdb=" SG CYS B4824 " distance=2.04 Simple disulfide: pdb=" SG CYS B4768 " - pdb=" SG CYS B4915 " distance=2.04 Simple disulfide: pdb=" SG CYS B4853 " - pdb=" SG CYS B5000 " distance=2.03 Simple disulfide: pdb=" SG CYS C4173 " - pdb=" SG CYS C4325 " distance=2.03 Simple disulfide: pdb=" SG CYS C4186 " - pdb=" SG CYS C4236 " distance=2.07 Simple disulfide: pdb=" SG CYS C4270 " - pdb=" SG CYS C4406 " distance=2.03 Simple disulfide: pdb=" SG CYS C4352 " - pdb=" SG CYS C4490 " distance=2.04 Simple disulfide: pdb=" SG CYS C4433 " - pdb=" SG CYS C4573 " distance=2.03 Simple disulfide: pdb=" SG CYS C4518 " - pdb=" SG CYS C4655 " distance=2.04 Simple disulfide: pdb=" SG CYS C4600 " - pdb=" SG CYS C4739 " distance=2.02 Simple disulfide: pdb=" SG CYS C4683 " - pdb=" SG CYS C4824 " distance=2.04 Simple disulfide: pdb=" SG CYS C4768 " - pdb=" SG CYS C4915 " distance=2.04 Simple disulfide: pdb=" SG CYS C4853 " - pdb=" SG CYS C5000 " distance=2.03 Simple disulfide: pdb=" SG CYS D4173 " - pdb=" SG CYS D4325 " distance=2.03 Simple disulfide: pdb=" SG CYS D4186 " - pdb=" SG CYS D4236 " distance=2.07 Simple disulfide: pdb=" SG CYS D4270 " - pdb=" SG CYS D4406 " distance=2.03 Simple disulfide: pdb=" SG CYS D4352 " - pdb=" SG CYS D4490 " distance=2.04 Simple disulfide: pdb=" SG CYS D4433 " - pdb=" SG CYS D4573 " distance=2.03 Simple disulfide: pdb=" SG CYS D4518 " - pdb=" SG CYS D4655 " distance=2.04 Simple disulfide: pdb=" SG CYS D4600 " - pdb=" SG CYS D4739 " distance=2.02 Simple disulfide: pdb=" SG CYS D4683 " - pdb=" SG CYS D4824 " distance=2.04 Simple disulfide: pdb=" SG CYS D4768 " - pdb=" SG CYS D4915 " distance=2.04 Simple disulfide: pdb=" SG CYS D4853 " - pdb=" SG CYS D5000 " distance=2.03 Simple disulfide: pdb=" SG CYS E4173 " - pdb=" SG CYS E4325 " distance=2.03 Simple disulfide: pdb=" SG CYS E4186 " - pdb=" SG CYS E4236 " distance=2.07 Simple disulfide: pdb=" SG CYS E4270 " - pdb=" SG CYS E4406 " distance=2.03 Simple disulfide: pdb=" SG CYS E4352 " - pdb=" SG CYS E4490 " distance=2.03 Simple disulfide: pdb=" SG CYS E4433 " - pdb=" SG CYS E4573 " distance=2.03 Simple disulfide: pdb=" SG CYS E4518 " - pdb=" SG CYS E4655 " distance=2.04 Simple disulfide: pdb=" SG CYS E4600 " - pdb=" SG CYS E4739 " distance=2.02 Simple disulfide: pdb=" SG CYS E4683 " - pdb=" SG CYS E4824 " distance=2.04 Simple disulfide: pdb=" SG CYS E4768 " - pdb=" SG CYS E4915 " distance=2.04 Simple disulfide: pdb=" SG CYS E4853 " - pdb=" SG CYS E5000 " distance=2.03 Simple disulfide: pdb=" SG CYS F4173 " - pdb=" SG CYS F4325 " distance=2.03 Simple disulfide: pdb=" SG CYS F4186 " - pdb=" SG CYS F4236 " distance=2.07 Simple disulfide: pdb=" SG CYS F4270 " - pdb=" SG CYS F4406 " distance=2.03 Simple disulfide: pdb=" SG CYS F4352 " - pdb=" SG CYS F4490 " distance=2.03 Simple disulfide: pdb=" SG CYS F4433 " - pdb=" SG CYS F4573 " distance=2.03 Simple disulfide: pdb=" SG CYS F4518 " - pdb=" SG CYS F4655 " distance=2.04 Simple disulfide: pdb=" SG CYS F4600 " - pdb=" SG CYS F4739 " distance=2.02 Simple disulfide: pdb=" SG CYS F4683 " - pdb=" SG CYS F4824 " distance=2.04 Simple disulfide: pdb=" SG CYS F4768 " - pdb=" SG CYS F4915 " distance=2.04 Simple disulfide: pdb=" SG CYS F4853 " - pdb=" SG CYS F5000 " distance=2.03 Simple disulfide: pdb=" SG CYS G4173 " - pdb=" SG CYS G4325 " distance=2.03 Simple disulfide: pdb=" SG CYS G4186 " - pdb=" SG CYS G4236 " distance=2.07 Simple disulfide: pdb=" SG CYS G4270 " - pdb=" SG CYS G4406 " distance=2.03 Simple disulfide: pdb=" SG CYS G4352 " - pdb=" SG CYS G4490 " distance=2.04 Simple disulfide: pdb=" SG CYS G4433 " - pdb=" SG CYS G4573 " distance=2.03 Simple disulfide: pdb=" SG CYS G4518 " - pdb=" SG CYS G4655 " distance=2.04 Simple disulfide: pdb=" SG CYS G4600 " - pdb=" SG CYS G4739 " distance=2.02 Simple disulfide: pdb=" SG CYS G4683 " - pdb=" SG CYS G4824 " distance=2.04 Simple disulfide: pdb=" SG CYS G4768 " - pdb=" SG CYS G4915 " distance=2.04 Simple disulfide: pdb=" SG CYS G4853 " - pdb=" SG CYS G5000 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11158 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 175 sheets defined 2.4% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 4389 through 4393 Processing helix chain 'A' and resid 4638 through 4642 Processing helix chain 'A' and resid 4723 through 4727 Processing helix chain 'A' and resid 4875 through 4880 Processing helix chain 'B' and resid 4389 through 4393 Processing helix chain 'B' and resid 4638 through 4642 Processing helix chain 'B' and resid 4723 through 4727 Processing helix chain 'B' and resid 4875 through 4880 Processing helix chain 'C' and resid 4389 through 4393 Processing helix chain 'C' and resid 4638 through 4642 Processing helix chain 'C' and resid 4723 through 4727 Processing helix chain 'C' and resid 4875 through 4880 Processing helix chain 'D' and resid 4389 through 4393 Processing helix chain 'D' and resid 4638 through 4642 Processing helix chain 'D' and resid 4723 through 4727 Processing helix chain 'D' and resid 4875 through 4880 Processing helix chain 'E' and resid 4389 through 4393 Processing helix chain 'E' and resid 4638 through 4642 Processing helix chain 'E' and resid 4723 through 4727 Processing helix chain 'E' and resid 4875 through 4880 Processing helix chain 'F' and resid 4389 through 4393 Processing helix chain 'F' and resid 4638 through 4642 Processing helix chain 'F' and resid 4723 through 4727 Processing helix chain 'F' and resid 4875 through 4880 Processing helix chain 'G' and resid 4389 through 4393 Processing helix chain 'G' and resid 4638 through 4642 Processing helix chain 'G' and resid 4723 through 4727 Processing helix chain 'G' and resid 4875 through 4880 Processing sheet with id=AA1, first strand: chain 'A' and resid 4166 through 4168 Processing sheet with id=AA2, first strand: chain 'A' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 4263 through 4264 Processing sheet with id=AA5, first strand: chain 'A' and resid 4273 through 4276 removed outlier: 5.876A pdb=" N GLY A4273 " --> pdb=" O ASN A4309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 4298 through 4300 Processing sheet with id=AA7, first strand: chain 'A' and resid 4298 through 4300 Processing sheet with id=AA8, first strand: chain 'A' and resid 4349 through 4352 removed outlier: 7.088A pdb=" N PHE A4349 " --> pdb=" O SER A4416 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS A4418 " --> pdb=" O PHE A4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A4351 " --> pdb=" O HIS A4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A4411 " --> pdb=" O LEU A4398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 4356 through 4357 Processing sheet with id=AB1, first strand: chain 'A' and resid 4426 through 4428 Processing sheet with id=AB2, first strand: chain 'A' and resid 4432 through 4433 removed outlier: 6.582A pdb=" N ILE A4432 " --> pdb=" O HIS A4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 4458 through 4461 removed outlier: 3.714A pdb=" N THR A4448 " --> pdb=" O MET A4485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER A4521 " --> pdb=" O ASN A4557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4546 through 4548 Processing sheet with id=AB6, first strand: chain 'A' and resid 4546 through 4548 Processing sheet with id=AB7, first strand: chain 'A' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE A4597 " --> pdb=" O VAL A4665 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A4667 " --> pdb=" O ILE A4597 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A4599 " --> pdb=" O ASN A4667 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4675 through 4679 removed outlier: 6.360A pdb=" N SER A4691 " --> pdb=" O VAL A4676 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN A4678 " --> pdb=" O VAL A4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A4689 " --> pdb=" O ASN A4678 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE A4682 " --> pdb=" O ASP A4752 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A4712 " --> pdb=" O TRP A4703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE A4682 " --> pdb=" O ASP A4752 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4765 through 4768 removed outlier: 7.410A pdb=" N ASP A4826 " --> pdb=" O ASN A4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN A4821 " --> pdb=" O ASP A4826 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4773 through 4774 Processing sheet with id=AC4, first strand: chain 'A' and resid 4850 through 4853 removed outlier: 6.359A pdb=" N GLN A4850 " --> pdb=" O ASN A4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP A4928 " --> pdb=" O GLN A4850 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A4852 " --> pdb=" O ASP A4928 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 4857 through 4860 removed outlier: 3.693A pdb=" N THR A4893 " --> pdb=" O LEU A4860 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 4949 through 4950 Processing sheet with id=AC7, first strand: chain 'A' and resid 4960 through 4965 removed outlier: 3.503A pdb=" N SER A5004 " --> pdb=" O LEU A4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN A4997 " --> pdb=" O ASN A5002 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A5002 " --> pdb=" O ASN A4997 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 4166 through 4168 Processing sheet with id=AC9, first strand: chain 'B' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 4263 through 4264 Processing sheet with id=AD3, first strand: chain 'B' and resid 4273 through 4276 removed outlier: 5.876A pdb=" N GLY B4273 " --> pdb=" O ASN B4309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 4298 through 4300 Processing sheet with id=AD5, first strand: chain 'B' and resid 4298 through 4300 Processing sheet with id=AD6, first strand: chain 'B' and resid 4349 through 4352 removed outlier: 7.088A pdb=" N PHE B4349 " --> pdb=" O SER B4416 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS B4418 " --> pdb=" O PHE B4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B4351 " --> pdb=" O HIS B4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B4411 " --> pdb=" O LEU B4398 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 4356 through 4357 Processing sheet with id=AD8, first strand: chain 'B' and resid 4426 through 4428 Processing sheet with id=AD9, first strand: chain 'B' and resid 4432 through 4433 removed outlier: 6.581A pdb=" N ILE B4432 " --> pdb=" O HIS B4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 4458 through 4461 removed outlier: 3.715A pdb=" N THR B4448 " --> pdb=" O MET B4485 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER B4521 " --> pdb=" O ASN B4557 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 4546 through 4548 Processing sheet with id=AE4, first strand: chain 'B' and resid 4546 through 4548 Processing sheet with id=AE5, first strand: chain 'B' and resid 4597 through 4600 removed outlier: 6.554A pdb=" N ILE B4597 " --> pdb=" O VAL B4665 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN B4667 " --> pdb=" O ILE B4597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B4599 " --> pdb=" O ASN B4667 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 4675 through 4679 removed outlier: 6.359A pdb=" N SER B4691 " --> pdb=" O VAL B4676 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B4678 " --> pdb=" O VAL B4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B4689 " --> pdb=" O ASN B4678 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE B4682 " --> pdb=" O ASP B4752 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B4712 " --> pdb=" O TRP B4703 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE B4682 " --> pdb=" O ASP B4752 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 4765 through 4768 removed outlier: 7.411A pdb=" N ASP B4826 " --> pdb=" O ASN B4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN B4821 " --> pdb=" O ASP B4826 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 4773 through 4774 Processing sheet with id=AF2, first strand: chain 'B' and resid 4850 through 4853 removed outlier: 6.358A pdb=" N GLN B4850 " --> pdb=" O ASN B4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP B4928 " --> pdb=" O GLN B4850 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU B4852 " --> pdb=" O ASP B4928 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 4857 through 4860 removed outlier: 3.692A pdb=" N THR B4893 " --> pdb=" O LEU B4860 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 4949 through 4950 Processing sheet with id=AF5, first strand: chain 'B' and resid 4960 through 4965 removed outlier: 3.504A pdb=" N SER B5004 " --> pdb=" O LEU B4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN B4997 " --> pdb=" O ASN B5002 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN B5002 " --> pdb=" O ASN B4997 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 4166 through 4168 Processing sheet with id=AF7, first strand: chain 'C' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 4263 through 4264 Processing sheet with id=AG1, first strand: chain 'C' and resid 4273 through 4276 removed outlier: 5.876A pdb=" N GLY C4273 " --> pdb=" O ASN C4309 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 4298 through 4300 Processing sheet with id=AG3, first strand: chain 'C' and resid 4298 through 4300 Processing sheet with id=AG4, first strand: chain 'C' and resid 4349 through 4352 removed outlier: 7.088A pdb=" N PHE C4349 " --> pdb=" O SER C4416 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS C4418 " --> pdb=" O PHE C4349 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C4351 " --> pdb=" O HIS C4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C4411 " --> pdb=" O LEU C4398 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 4356 through 4357 Processing sheet with id=AG6, first strand: chain 'C' and resid 4426 through 4428 Processing sheet with id=AG7, first strand: chain 'C' and resid 4432 through 4433 removed outlier: 6.582A pdb=" N ILE C4432 " --> pdb=" O HIS C4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 4458 through 4461 removed outlier: 3.713A pdb=" N THR C4448 " --> pdb=" O MET C4485 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER C4521 " --> pdb=" O ASN C4557 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 4546 through 4548 Processing sheet with id=AH2, first strand: chain 'C' and resid 4546 through 4548 Processing sheet with id=AH3, first strand: chain 'C' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE C4597 " --> pdb=" O VAL C4665 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN C4667 " --> pdb=" O ILE C4597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C4599 " --> pdb=" O ASN C4667 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 4675 through 4679 removed outlier: 6.361A pdb=" N SER C4691 " --> pdb=" O VAL C4676 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C4678 " --> pdb=" O VAL C4689 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C4689 " --> pdb=" O ASN C4678 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE C4682 " --> pdb=" O ASP C4752 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY C4712 " --> pdb=" O TRP C4703 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE C4682 " --> pdb=" O ASP C4752 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 4765 through 4768 removed outlier: 7.410A pdb=" N ASP C4826 " --> pdb=" O ASN C4821 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN C4821 " --> pdb=" O ASP C4826 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 4773 through 4774 Processing sheet with id=AH9, first strand: chain 'C' and resid 4850 through 4853 removed outlier: 6.359A pdb=" N GLN C4850 " --> pdb=" O ASN C4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP C4928 " --> pdb=" O GLN C4850 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C4852 " --> pdb=" O ASP C4928 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 4857 through 4860 removed outlier: 3.693A pdb=" N THR C4893 " --> pdb=" O LEU C4860 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 4949 through 4950 Processing sheet with id=AI3, first strand: chain 'C' and resid 4960 through 4965 removed outlier: 3.503A pdb=" N SER C5004 " --> pdb=" O LEU C4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN C4997 " --> pdb=" O ASN C5002 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN C5002 " --> pdb=" O ASN C4997 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 4166 through 4168 Processing sheet with id=AI5, first strand: chain 'D' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 4263 through 4264 Processing sheet with id=AI8, first strand: chain 'D' and resid 4273 through 4276 removed outlier: 5.875A pdb=" N GLY D4273 " --> pdb=" O ASN D4309 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 4298 through 4300 Processing sheet with id=AJ1, first strand: chain 'D' and resid 4298 through 4300 Processing sheet with id=AJ2, first strand: chain 'D' and resid 4349 through 4352 removed outlier: 7.087A pdb=" N PHE D4349 " --> pdb=" O SER D4416 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS D4418 " --> pdb=" O PHE D4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D4351 " --> pdb=" O HIS D4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D4411 " --> pdb=" O LEU D4398 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 4356 through 4357 Processing sheet with id=AJ4, first strand: chain 'D' and resid 4426 through 4428 Processing sheet with id=AJ5, first strand: chain 'D' and resid 4432 through 4433 removed outlier: 6.582A pdb=" N ILE D4432 " --> pdb=" O HIS D4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'D' and resid 4458 through 4461 removed outlier: 3.713A pdb=" N THR D4448 " --> pdb=" O MET D4485 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER D4521 " --> pdb=" O ASN D4557 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 4546 through 4548 Processing sheet with id=AJ9, first strand: chain 'D' and resid 4546 through 4548 Processing sheet with id=AK1, first strand: chain 'D' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE D4597 " --> pdb=" O VAL D4665 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN D4667 " --> pdb=" O ILE D4597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL D4599 " --> pdb=" O ASN D4667 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 4675 through 4679 removed outlier: 6.361A pdb=" N SER D4691 " --> pdb=" O VAL D4676 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN D4678 " --> pdb=" O VAL D4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D4689 " --> pdb=" O ASN D4678 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE D4682 " --> pdb=" O ASP D4752 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D4712 " --> pdb=" O TRP D4703 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE D4682 " --> pdb=" O ASP D4752 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 4765 through 4768 removed outlier: 7.410A pdb=" N ASP D4826 " --> pdb=" O ASN D4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN D4821 " --> pdb=" O ASP D4826 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 4773 through 4774 Processing sheet with id=AK7, first strand: chain 'D' and resid 4850 through 4853 removed outlier: 6.358A pdb=" N GLN D4850 " --> pdb=" O ASN D4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP D4928 " --> pdb=" O GLN D4850 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D4852 " --> pdb=" O ASP D4928 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 4857 through 4860 removed outlier: 3.693A pdb=" N THR D4893 " --> pdb=" O LEU D4860 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 4949 through 4950 Processing sheet with id=AL1, first strand: chain 'D' and resid 4960 through 4965 removed outlier: 3.503A pdb=" N SER D5004 " --> pdb=" O LEU D4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN D4997 " --> pdb=" O ASN D5002 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN D5002 " --> pdb=" O ASN D4997 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'E' and resid 4166 through 4168 Processing sheet with id=AL3, first strand: chain 'E' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'E' and resid 4263 through 4264 Processing sheet with id=AL6, first strand: chain 'E' and resid 4273 through 4276 removed outlier: 5.876A pdb=" N GLY E4273 " --> pdb=" O ASN E4309 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'E' and resid 4298 through 4300 Processing sheet with id=AL8, first strand: chain 'E' and resid 4298 through 4300 Processing sheet with id=AL9, first strand: chain 'E' and resid 4349 through 4352 removed outlier: 7.088A pdb=" N PHE E4349 " --> pdb=" O SER E4416 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS E4418 " --> pdb=" O PHE E4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E4351 " --> pdb=" O HIS E4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR E4411 " --> pdb=" O LEU E4398 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'E' and resid 4356 through 4357 Processing sheet with id=AM2, first strand: chain 'E' and resid 4426 through 4428 Processing sheet with id=AM3, first strand: chain 'E' and resid 4432 through 4433 removed outlier: 6.582A pdb=" N ILE E4432 " --> pdb=" O HIS E4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'E' and resid 4458 through 4461 removed outlier: 3.714A pdb=" N THR E4448 " --> pdb=" O MET E4485 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 4521 through 4524 removed outlier: 5.954A pdb=" N SER E4521 " --> pdb=" O ASN E4557 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'E' and resid 4546 through 4548 Processing sheet with id=AM7, first strand: chain 'E' and resid 4546 through 4548 Processing sheet with id=AM8, first strand: chain 'E' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE E4597 " --> pdb=" O VAL E4665 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN E4667 " --> pdb=" O ILE E4597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E4599 " --> pdb=" O ASN E4667 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'E' and resid 4675 through 4679 removed outlier: 6.360A pdb=" N SER E4691 " --> pdb=" O VAL E4676 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN E4678 " --> pdb=" O VAL E4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E4689 " --> pdb=" O ASN E4678 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'E' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE E4682 " --> pdb=" O ASP E4752 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY E4712 " --> pdb=" O TRP E4703 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'E' and resid 4681 through 4683 removed outlier: 7.093A pdb=" N ILE E4682 " --> pdb=" O ASP E4752 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'E' and resid 4765 through 4768 removed outlier: 7.409A pdb=" N ASP E4826 " --> pdb=" O ASN E4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN E4821 " --> pdb=" O ASP E4826 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'E' and resid 4773 through 4774 Processing sheet with id=AN5, first strand: chain 'E' and resid 4850 through 4853 removed outlier: 6.359A pdb=" N GLN E4850 " --> pdb=" O ASN E4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP E4928 " --> pdb=" O GLN E4850 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E4852 " --> pdb=" O ASP E4928 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'E' and resid 4857 through 4860 removed outlier: 3.693A pdb=" N THR E4893 " --> pdb=" O LEU E4860 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'E' and resid 4949 through 4950 Processing sheet with id=AN8, first strand: chain 'E' and resid 4960 through 4965 removed outlier: 3.503A pdb=" N SER E5004 " --> pdb=" O LEU E4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN E4997 " --> pdb=" O ASN E5002 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN E5002 " --> pdb=" O ASN E4997 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'F' and resid 4166 through 4168 Processing sheet with id=AO1, first strand: chain 'F' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'F' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'F' and resid 4263 through 4264 Processing sheet with id=AO4, first strand: chain 'F' and resid 4273 through 4276 removed outlier: 5.875A pdb=" N GLY F4273 " --> pdb=" O ASN F4309 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'F' and resid 4298 through 4300 Processing sheet with id=AO6, first strand: chain 'F' and resid 4298 through 4300 Processing sheet with id=AO7, first strand: chain 'F' and resid 4349 through 4352 removed outlier: 7.088A pdb=" N PHE F4349 " --> pdb=" O SER F4416 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N HIS F4418 " --> pdb=" O PHE F4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F4351 " --> pdb=" O HIS F4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F4411 " --> pdb=" O LEU F4398 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'F' and resid 4356 through 4357 Processing sheet with id=AO9, first strand: chain 'F' and resid 4426 through 4428 Processing sheet with id=AP1, first strand: chain 'F' and resid 4432 through 4433 removed outlier: 6.583A pdb=" N ILE F4432 " --> pdb=" O HIS F4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP1 Processing sheet with id=AP2, first strand: chain 'F' and resid 4458 through 4461 removed outlier: 3.713A pdb=" N THR F4448 " --> pdb=" O MET F4485 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'F' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER F4521 " --> pdb=" O ASN F4557 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'F' and resid 4546 through 4548 Processing sheet with id=AP5, first strand: chain 'F' and resid 4546 through 4548 Processing sheet with id=AP6, first strand: chain 'F' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE F4597 " --> pdb=" O VAL F4665 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN F4667 " --> pdb=" O ILE F4597 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL F4599 " --> pdb=" O ASN F4667 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'F' and resid 4675 through 4679 removed outlier: 6.360A pdb=" N SER F4691 " --> pdb=" O VAL F4676 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F4678 " --> pdb=" O VAL F4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F4689 " --> pdb=" O ASN F4678 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'F' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE F4682 " --> pdb=" O ASP F4752 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY F4712 " --> pdb=" O TRP F4703 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'F' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE F4682 " --> pdb=" O ASP F4752 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'F' and resid 4765 through 4768 removed outlier: 7.409A pdb=" N ASP F4826 " --> pdb=" O ASN F4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN F4821 " --> pdb=" O ASP F4826 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'F' and resid 4773 through 4774 Processing sheet with id=AQ3, first strand: chain 'F' and resid 4850 through 4853 removed outlier: 6.360A pdb=" N GLN F4850 " --> pdb=" O ASN F4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP F4928 " --> pdb=" O GLN F4850 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU F4852 " --> pdb=" O ASP F4928 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'F' and resid 4857 through 4860 removed outlier: 3.693A pdb=" N THR F4893 " --> pdb=" O LEU F4860 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'F' and resid 4949 through 4950 Processing sheet with id=AQ6, first strand: chain 'F' and resid 4960 through 4965 removed outlier: 3.503A pdb=" N SER F5004 " --> pdb=" O LEU F4995 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASN F4997 " --> pdb=" O ASN F5002 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN F5002 " --> pdb=" O ASN F4997 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'G' and resid 4166 through 4168 Processing sheet with id=AQ8, first strand: chain 'G' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'G' and resid 4171 through 4173 removed outlier: 6.833A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'G' and resid 4263 through 4264 Processing sheet with id=AR2, first strand: chain 'G' and resid 4273 through 4276 removed outlier: 5.875A pdb=" N GLY G4273 " --> pdb=" O ASN G4309 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'G' and resid 4298 through 4300 Processing sheet with id=AR4, first strand: chain 'G' and resid 4298 through 4300 Processing sheet with id=AR5, first strand: chain 'G' and resid 4349 through 4352 removed outlier: 7.087A pdb=" N PHE G4349 " --> pdb=" O SER G4416 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N HIS G4418 " --> pdb=" O PHE G4349 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G4351 " --> pdb=" O HIS G4418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR G4411 " --> pdb=" O LEU G4398 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'G' and resid 4356 through 4357 Processing sheet with id=AR7, first strand: chain 'G' and resid 4426 through 4428 Processing sheet with id=AR8, first strand: chain 'G' and resid 4432 through 4433 removed outlier: 6.582A pdb=" N ILE G4432 " --> pdb=" O HIS G4503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR8 Processing sheet with id=AR9, first strand: chain 'G' and resid 4458 through 4461 removed outlier: 3.714A pdb=" N THR G4448 " --> pdb=" O MET G4485 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'G' and resid 4521 through 4524 removed outlier: 5.953A pdb=" N SER G4521 " --> pdb=" O ASN G4557 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'G' and resid 4546 through 4548 Processing sheet with id=AS3, first strand: chain 'G' and resid 4546 through 4548 Processing sheet with id=AS4, first strand: chain 'G' and resid 4597 through 4600 removed outlier: 6.555A pdb=" N ILE G4597 " --> pdb=" O VAL G4665 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN G4667 " --> pdb=" O ILE G4597 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL G4599 " --> pdb=" O ASN G4667 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'G' and resid 4675 through 4679 removed outlier: 6.361A pdb=" N SER G4691 " --> pdb=" O VAL G4676 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN G4678 " --> pdb=" O VAL G4689 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G4689 " --> pdb=" O ASN G4678 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'G' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE G4682 " --> pdb=" O ASP G4752 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY G4712 " --> pdb=" O TRP G4703 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'G' and resid 4681 through 4683 removed outlier: 7.092A pdb=" N ILE G4682 " --> pdb=" O ASP G4752 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'G' and resid 4765 through 4768 removed outlier: 7.409A pdb=" N ASP G4826 " --> pdb=" O ASN G4821 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN G4821 " --> pdb=" O ASP G4826 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'G' and resid 4773 through 4774 Processing sheet with id=AT1, first strand: chain 'G' and resid 4850 through 4853 removed outlier: 6.359A pdb=" N GLN G4850 " --> pdb=" O ASN G4926 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP G4928 " --> pdb=" O GLN G4850 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G4852 " --> pdb=" O ASP G4928 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'G' and resid 4857 through 4860 removed outlier: 3.692A pdb=" N THR G4893 " --> pdb=" O LEU G4860 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'G' and resid 4949 through 4950 Processing sheet with id=AT4, first strand: chain 'G' and resid 4960 through 4965 removed outlier: 3.502A pdb=" N SER G5004 " --> pdb=" O LEU G4995 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN G4997 " --> pdb=" O ASN G5002 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN G5002 " --> pdb=" O ASN G4997 " (cutoff:3.500A) 1456 hydrogen bonds defined for protein. 3402 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: 17.85 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 11485 1.32 - 1.46: 12919 1.46 - 1.59: 19731 1.59 - 1.72: 7 1.72 - 1.86: 231 Bond restraints: 44373 Sorted by residual: bond pdb=" CA GLN D4154 " pdb=" C GLN D4154 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.18e-02 7.18e+03 5.20e+01 bond pdb=" CA GLN E4154 " pdb=" C GLN E4154 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.18e-02 7.18e+03 4.75e+01 bond pdb=" CA GLN F4154 " pdb=" C GLN F4154 " ideal model delta sigma weight residual 1.523 1.443 0.081 1.18e-02 7.18e+03 4.67e+01 bond pdb=" CA GLN G4154 " pdb=" C GLN G4154 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.18e-02 7.18e+03 4.45e+01 bond pdb=" CA GLN B4154 " pdb=" C GLN B4154 " ideal model delta sigma weight residual 1.523 1.445 0.079 1.18e-02 7.18e+03 4.44e+01 ... (remaining 44368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 57232 2.89 - 5.77: 3801 5.77 - 8.66: 343 8.66 - 11.54: 42 11.54 - 14.43: 14 Bond angle restraints: 61432 Sorted by residual: angle pdb=" C GLN C4154 " pdb=" N VAL C4155 " pdb=" CA VAL C4155 " ideal model delta sigma weight residual 122.98 108.55 14.43 1.42e+00 4.96e-01 1.03e+02 angle pdb=" C GLN G4154 " pdb=" N VAL G4155 " pdb=" CA VAL G4155 " ideal model delta sigma weight residual 122.98 108.56 14.42 1.42e+00 4.96e-01 1.03e+02 angle pdb=" C GLN A4154 " pdb=" N VAL A4155 " pdb=" CA VAL A4155 " ideal model delta sigma weight residual 122.98 108.57 14.41 1.42e+00 4.96e-01 1.03e+02 angle pdb=" C GLN D4154 " pdb=" N VAL D4155 " pdb=" CA VAL D4155 " ideal model delta sigma weight residual 122.98 108.58 14.40 1.42e+00 4.96e-01 1.03e+02 angle pdb=" C GLN F4154 " pdb=" N VAL F4155 " pdb=" CA VAL F4155 " ideal model delta sigma weight residual 122.98 108.58 14.40 1.42e+00 4.96e-01 1.03e+02 ... (remaining 61427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 25113 16.78 - 33.56: 745 33.56 - 50.35: 70 50.35 - 67.13: 105 67.13 - 83.91: 35 Dihedral angle restraints: 26068 sinusoidal: 8722 harmonic: 17346 Sorted by residual: dihedral pdb=" CB CYS D4518 " pdb=" SG CYS D4518 " pdb=" SG CYS D4655 " pdb=" CB CYS D4655 " ideal model delta sinusoidal sigma weight residual 93.00 158.83 -65.83 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS E4518 " pdb=" SG CYS E4518 " pdb=" SG CYS E4655 " pdb=" CB CYS E4655 " ideal model delta sinusoidal sigma weight residual 93.00 158.80 -65.80 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS C4518 " pdb=" SG CYS C4518 " pdb=" SG CYS C4655 " pdb=" CB CYS C4655 " ideal model delta sinusoidal sigma weight residual 93.00 158.80 -65.80 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 26065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5220 0.071 - 0.142: 2135 0.142 - 0.214: 346 0.214 - 0.285: 27 0.285 - 0.356: 35 Chirality restraints: 7763 Sorted by residual: chirality pdb=" CA TYR C4731 " pdb=" N TYR C4731 " pdb=" C TYR C4731 " pdb=" CB TYR C4731 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA TYR D4731 " pdb=" N TYR D4731 " pdb=" C TYR D4731 " pdb=" CB TYR D4731 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA TYR F4731 " pdb=" N TYR F4731 " pdb=" C TYR F4731 " pdb=" CB TYR F4731 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 7760 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D4656 " 0.537 9.50e-02 1.11e+02 2.41e-01 3.56e+01 pdb=" NE ARG D4656 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG D4656 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D4656 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D4656 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F4656 " 0.537 9.50e-02 1.11e+02 2.41e-01 3.55e+01 pdb=" NE ARG F4656 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG F4656 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F4656 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F4656 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4656 " -0.537 9.50e-02 1.11e+02 2.41e-01 3.55e+01 pdb=" NE ARG A4656 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A4656 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A4656 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A4656 " -0.020 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 35 1.82 - 2.59: 552 2.59 - 3.36: 54297 3.36 - 4.13: 109292 4.13 - 4.90: 182571 Nonbonded interactions: 346747 Sorted by model distance: nonbonded pdb=" CE2 PHE C4954 " pdb=" OD2 ASP D4973 " model vdw 1.048 3.340 nonbonded pdb=" CE2 PHE B4954 " pdb=" OD2 ASP C4973 " model vdw 1.057 3.340 nonbonded pdb=" CE2 PHE E4954 " pdb=" OD2 ASP F4973 " model vdw 1.063 3.340 nonbonded pdb=" CE2 PHE F4954 " pdb=" OD2 ASP G4973 " model vdw 1.068 3.340 nonbonded pdb=" CE2 PHE A4954 " pdb=" OD2 ASP B4973 " model vdw 1.070 3.340 ... (remaining 346742 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: 0.16 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 53.170 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.120 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.018 0.168 44443 Z= 0.914 Angle : 1.564 14.425 61572 Z= 1.026 Chirality : 0.075 0.356 7763 Planarity : 0.011 0.241 7980 Dihedral : 9.818 83.910 14700 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.47 % 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 aren not related in a simple way. whole: 0.76 (0.10), residues: 5999 helix: -4.19 (0.14), residues: 42 sheet: 0.81 (0.11), residues: 1981 loop : 0.51 (0.09), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D4450 TYR 0.045 0.006 TYR B4227 PHE 0.079 0.008 PHE C4349 TRP 0.029 0.007 TRP B4817 HIS 0.011 0.005 HIS G4585 Details of bonding type rmsd covalent geometry : bond 0.01782 (44373) covalent geometry : angle 1.56223 (61432) SS BOND : bond 0.01544 ( 70) SS BOND : angle 2.28491 ( 140) hydrogen bonds : bond 0.17357 ( 1288) hydrogen bonds : angle 8.21671 ( 3402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4154 GLN cc_start: 0.8155 (pt0) cc_final: 0.7648 (mm110) REVERT: A 4718 THR cc_start: 0.8809 (m) cc_final: 0.8598 (p) REVERT: A 4791 SER cc_start: 0.8713 (m) cc_final: 0.8470 (p) REVERT: B 4154 GLN cc_start: 0.8103 (pt0) cc_final: 0.7682 (mm-40) REVERT: B 4432 ILE cc_start: 0.7871 (mt) cc_final: 0.7608 (tt) REVERT: B 4483 MET cc_start: 0.8552 (ttm) cc_final: 0.8329 (ttm) REVERT: B 4657 SER cc_start: 0.8691 (p) cc_final: 0.8377 (t) REVERT: B 4675 ILE cc_start: 0.8428 (mt) cc_final: 0.8201 (mt) REVERT: B 4791 SER cc_start: 0.8616 (m) cc_final: 0.8246 (p) REVERT: C 4154 GLN cc_start: 0.8252 (pt0) cc_final: 0.7433 (mm110) REVERT: C 4483 MET cc_start: 0.8763 (ttm) cc_final: 0.8105 (ttt) REVERT: D 4154 GLN cc_start: 0.7960 (pt0) cc_final: 0.7715 (tp40) REVERT: D 4432 ILE cc_start: 0.8120 (mt) cc_final: 0.7750 (tt) REVERT: D 4483 MET cc_start: 0.8683 (ttm) cc_final: 0.8417 (ttt) REVERT: D 4644 LYS cc_start: 0.9344 (tttt) cc_final: 0.9012 (ttmm) REVERT: D 4647 LEU cc_start: 0.8371 (tp) cc_final: 0.7580 (tp) REVERT: D 4775 LEU cc_start: 0.8398 (mt) cc_final: 0.8184 (mt) REVERT: D 4832 MET cc_start: 0.8135 (tmm) cc_final: 0.7443 (tmm) REVERT: E 4432 ILE cc_start: 0.8037 (mt) cc_final: 0.7815 (tt) REVERT: E 4483 MET cc_start: 0.8772 (ttm) cc_final: 0.8224 (ttt) REVERT: E 4657 SER cc_start: 0.9022 (p) cc_final: 0.8773 (t) REVERT: E 4791 SER cc_start: 0.8416 (m) cc_final: 0.8105 (p) REVERT: F 4483 MET cc_start: 0.8603 (ttm) cc_final: 0.8244 (ttm) REVERT: F 4791 SER cc_start: 0.8705 (m) cc_final: 0.8419 (p) REVERT: G 4154 GLN cc_start: 0.7899 (pt0) cc_final: 0.7511 (mm110) REVERT: G 4483 MET cc_start: 0.8606 (ttm) cc_final: 0.7986 (ttt) REVERT: G 4644 LYS cc_start: 0.9244 (tttt) cc_final: 0.8737 (ttmm) REVERT: G 4791 SER cc_start: 0.8657 (m) cc_final: 0.8352 (p) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.2297 time to fit residues: 208.5970 Evaluate side-chains 186 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.6980 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4302 ASN A4509 GLN A4781 ASN A4986 GLN ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4302 ASN B4509 GLN B4781 ASN B4986 GLN ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4509 GLN C4781 ASN ** D4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4781 ASN D4986 GLN ** E4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4404 ASN E4509 GLN E4571 ASN E4781 ASN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4302 ASN F4585 HIS F4781 ASN ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4255 ASN G4585 HIS G4781 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075404 restraints weight = 89148.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077615 restraints weight = 44552.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079053 restraints weight = 26063.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080010 restraints weight = 17047.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080639 restraints weight = 12118.528| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44443 Z= 0.188 Angle : 0.652 11.052 61572 Z= 0.367 Chirality : 0.047 0.170 7763 Planarity : 0.005 0.060 7980 Dihedral : 5.433 23.191 6216 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.25 % Allowed : 4.46 % Favored : 94.29 % 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 aren not related in a simple way. whole: 0.73 (0.11), residues: 5999 helix: -3.78 (0.23), residues: 42 sheet: 0.65 (0.11), residues: 2338 loop : 0.56 (0.10), residues: 3619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G4656 TYR 0.016 0.002 TYR B4904 PHE 0.042 0.002 PHE C4954 TRP 0.020 0.002 TRP B4618 HIS 0.003 0.001 HIS C4418 Details of bonding type rmsd covalent geometry : bond 0.00399 (44373) covalent geometry : angle 0.64731 (61432) SS BOND : bond 0.00994 ( 70) SS BOND : angle 1.77927 ( 140) hydrogen bonds : bond 0.04981 ( 1288) hydrogen bonds : angle 6.31693 ( 3402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: B 4656 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7880 (ttt90) REVERT: B 4791 SER cc_start: 0.8691 (m) cc_final: 0.8361 (p) REVERT: B 4973 ASP cc_start: 0.8054 (t0) cc_final: 0.7798 (t0) REVERT: B 4976 LEU cc_start: 0.9236 (mt) cc_final: 0.8831 (mt) REVERT: C 4154 GLN cc_start: 0.7477 (pt0) cc_final: 0.7200 (mm110) REVERT: C 4172 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 4795 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8388 (mt) REVERT: C 4976 LEU cc_start: 0.9121 (mt) cc_final: 0.8483 (mt) REVERT: D 4775 LEU cc_start: 0.8487 (mt) cc_final: 0.8258 (mt) REVERT: E 4432 ILE cc_start: 0.7908 (mt) cc_final: 0.7245 (tt) REVERT: E 4483 MET cc_start: 0.8334 (ttm) cc_final: 0.7928 (ttt) REVERT: E 4973 ASP cc_start: 0.7629 (t0) cc_final: 0.7033 (t0) REVERT: E 4976 LEU cc_start: 0.9109 (mt) cc_final: 0.8145 (mt) REVERT: F 4791 SER cc_start: 0.8657 (m) cc_final: 0.8353 (p) REVERT: F 4832 MET cc_start: 0.8268 (tmm) cc_final: 0.7804 (tmm) REVERT: F 4973 ASP cc_start: 0.7838 (t0) cc_final: 0.7524 (t0) REVERT: F 4976 LEU cc_start: 0.9158 (mt) cc_final: 0.8687 (mt) REVERT: G 4154 GLN cc_start: 0.7569 (pt0) cc_final: 0.7087 (mm110) REVERT: G 4455 ASP cc_start: 0.7565 (t0) cc_final: 0.7329 (t0) REVERT: G 4644 LYS cc_start: 0.9144 (tttt) cc_final: 0.8797 (ttmm) REVERT: G 4791 SER cc_start: 0.8662 (m) cc_final: 0.8400 (p) REVERT: G 4973 ASP cc_start: 0.8109 (t0) cc_final: 0.7727 (t0) REVERT: G 4976 LEU cc_start: 0.9081 (mt) cc_final: 0.8356 (mt) outliers start: 63 outliers final: 29 residues processed: 287 average time/residue: 0.2316 time to fit residues: 118.1041 Evaluate side-chains 199 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4172 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4410 ASP Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain C residue 4172 ILE Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4860 LEU Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4835 GLU Chi-restraints excluded: chain D residue 4943 LEU Chi-restraints excluded: chain E residue 4245 SER Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4410 ASP Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4984 LEU Chi-restraints excluded: chain G residue 4172 ILE Chi-restraints excluded: chain G residue 4390 LEU Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4568 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 494 optimal weight: 10.0000 chunk 549 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 471 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 407 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 266 optimal weight: 0.0980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4255 ASN A4323 ASN A4509 GLN ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4488 ASN B4797 ASN ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4509 GLN C4797 ASN D4188 GLN ** D4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4509 GLN ** D4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4488 ASN E4797 ASN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4488 ASN ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4488 ASN G4797 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.069129 restraints weight = 92310.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.070914 restraints weight = 48528.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.072098 restraints weight = 29590.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.072911 restraints weight = 19996.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073447 restraints weight = 14493.910| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 44443 Z= 0.309 Angle : 0.720 10.052 61572 Z= 0.388 Chirality : 0.049 0.220 7763 Planarity : 0.005 0.081 7980 Dihedral : 5.540 25.499 6216 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.31 % Allowed : 5.09 % Favored : 92.60 % 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 aren not related in a simple way. whole: 0.29 (0.10), residues: 5999 helix: -3.78 (0.31), residues: 84 sheet: 0.23 (0.10), residues: 2450 loop : 0.41 (0.10), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B4656 TYR 0.020 0.002 TYR B4918 PHE 0.026 0.003 PHE B4827 TRP 0.020 0.003 TRP E4618 HIS 0.010 0.002 HIS A4418 Details of bonding type rmsd covalent geometry : bond 0.00702 (44373) covalent geometry : angle 0.71477 (61432) SS BOND : bond 0.00262 ( 70) SS BOND : angle 1.97118 ( 140) hydrogen bonds : bond 0.05060 ( 1288) hydrogen bonds : angle 5.90374 ( 3402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 172 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 4264 PHE cc_start: 0.8736 (m-80) cc_final: 0.8489 (m-10) REVERT: A 4806 TYR cc_start: 0.8274 (p90) cc_final: 0.8058 (p90) REVERT: B 4246 GLU cc_start: 0.7949 (mp0) cc_final: 0.7454 (mp0) REVERT: B 4353 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8039 (tt0) REVERT: B 4391 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8702 (t) REVERT: B 4656 ARG cc_start: 0.8455 (ttt-90) cc_final: 0.8215 (ttt90) REVERT: B 4791 SER cc_start: 0.8574 (m) cc_final: 0.8242 (p) REVERT: C 4154 GLN cc_start: 0.7663 (pt0) cc_final: 0.7167 (mm110) REVERT: C 4172 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8707 (mm) REVERT: C 4644 LYS cc_start: 0.9166 (tttt) cc_final: 0.8879 (tttm) REVERT: C 4976 LEU cc_start: 0.9393 (mt) cc_final: 0.8894 (mt) REVERT: D 4775 LEU cc_start: 0.9005 (mt) cc_final: 0.8784 (mt) REVERT: E 4432 ILE cc_start: 0.8210 (mt) cc_final: 0.7442 (tt) REVERT: E 4973 ASP cc_start: 0.7976 (t0) cc_final: 0.7403 (t0) REVERT: E 4976 LEU cc_start: 0.9362 (mt) cc_final: 0.8228 (mt) REVERT: F 4973 ASP cc_start: 0.7900 (t0) cc_final: 0.7353 (t0) REVERT: F 4976 LEU cc_start: 0.9319 (mt) cc_final: 0.8744 (mt) REVERT: G 4154 GLN cc_start: 0.7427 (pt0) cc_final: 0.6804 (mm110) REVERT: G 4455 ASP cc_start: 0.7495 (t0) cc_final: 0.7287 (t0) REVERT: G 4644 LYS cc_start: 0.9244 (tttt) cc_final: 0.8769 (ttmm) REVERT: G 4791 SER cc_start: 0.8655 (m) cc_final: 0.8365 (p) REVERT: G 4973 ASP cc_start: 0.8374 (t0) cc_final: 0.7981 (t0) REVERT: G 4976 LEU cc_start: 0.9237 (mt) cc_final: 0.8390 (mt) outliers start: 116 outliers final: 79 residues processed: 278 average time/residue: 0.2262 time to fit residues: 112.4569 Evaluate side-chains 220 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 139 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4172 ILE Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4310 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4560 THR Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4827 PHE Chi-restraints excluded: chain A residue 4878 GLN Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4976 LEU Chi-restraints excluded: chain A residue 4984 LEU Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4245 SER Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4391 VAL Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4718 THR Chi-restraints excluded: chain B residue 4827 PHE Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4999 THR Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4172 ILE Chi-restraints excluded: chain C residue 4254 ILE Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4378 SER Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4626 SER Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4765 ILE Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4827 PHE Chi-restraints excluded: chain C residue 4860 LEU Chi-restraints excluded: chain C residue 4999 THR Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4448 THR Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4680 THR Chi-restraints excluded: chain D residue 4827 PHE Chi-restraints excluded: chain D residue 4835 GLU Chi-restraints excluded: chain D residue 4860 LEU Chi-restraints excluded: chain D residue 4943 LEU Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4245 SER Chi-restraints excluded: chain E residue 4355 ASP Chi-restraints excluded: chain E residue 4378 SER Chi-restraints excluded: chain E residue 4448 THR Chi-restraints excluded: chain E residue 4560 THR Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4827 PHE Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4254 ILE Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4391 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4827 PHE Chi-restraints excluded: chain F residue 4984 LEU Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4172 ILE Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4718 THR Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4835 GLU Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 49 optimal weight: 0.8980 chunk 539 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 396 optimal weight: 2.9990 chunk 455 optimal weight: 0.6980 chunk 513 optimal weight: 5.9990 chunk 208 optimal weight: 0.5980 chunk 390 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4323 ASN A4797 ASN ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4190 GLN D4188 GLN D4190 GLN D4414 GLN D4797 ASN E4302 ASN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071373 restraints weight = 90718.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.073156 restraints weight = 47549.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074354 restraints weight = 28946.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.075149 restraints weight = 19469.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075701 restraints weight = 14164.302| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44443 Z= 0.142 Angle : 0.554 7.684 61572 Z= 0.298 Chirality : 0.045 0.176 7763 Planarity : 0.004 0.073 7980 Dihedral : 5.025 25.114 6216 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.55 % Allowed : 6.45 % Favored : 92.00 % 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 aren not related in a simple way. whole: 0.39 (0.11), residues: 5999 helix: -3.76 (0.30), residues: 84 sheet: 0.32 (0.10), residues: 2485 loop : 0.47 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F4656 TYR 0.019 0.002 TYR D4648 PHE 0.014 0.001 PHE B4264 TRP 0.014 0.002 TRP E4618 HIS 0.003 0.001 HIS D4418 Details of bonding type rmsd covalent geometry : bond 0.00322 (44373) covalent geometry : angle 0.55210 (61432) SS BOND : bond 0.00136 ( 70) SS BOND : angle 1.03203 ( 140) hydrogen bonds : bond 0.03837 ( 1288) hydrogen bonds : angle 5.56171 ( 3402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 185 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4246 GLU cc_start: 0.7915 (mp0) cc_final: 0.7321 (mp0) REVERT: B 4656 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8209 (ttt90) REVERT: B 4791 SER cc_start: 0.8642 (m) cc_final: 0.8281 (p) REVERT: C 4154 GLN cc_start: 0.7617 (pt0) cc_final: 0.7166 (mm110) REVERT: C 4644 LYS cc_start: 0.9167 (tttt) cc_final: 0.8947 (tttm) REVERT: C 4973 ASP cc_start: 0.7298 (t0) cc_final: 0.6814 (t0) REVERT: C 4976 LEU cc_start: 0.9366 (mt) cc_final: 0.8945 (mt) REVERT: E 4432 ILE cc_start: 0.7916 (mt) cc_final: 0.7313 (tt) REVERT: G 4154 GLN cc_start: 0.7393 (pt0) cc_final: 0.6784 (mm110) REVERT: G 4455 ASP cc_start: 0.7389 (t0) cc_final: 0.7160 (t0) REVERT: G 4644 LYS cc_start: 0.9161 (tttt) cc_final: 0.8661 (tttp) REVERT: G 4791 SER cc_start: 0.8855 (m) cc_final: 0.8534 (p) REVERT: G 4973 ASP cc_start: 0.8048 (t0) cc_final: 0.7708 (t0) REVERT: G 4976 LEU cc_start: 0.9254 (mt) cc_final: 0.8421 (mt) outliers start: 78 outliers final: 55 residues processed: 254 average time/residue: 0.2170 time to fit residues: 99.3273 Evaluate side-chains 207 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4791 SER Chi-restraints excluded: chain A residue 4860 LEU Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain B residue 4245 SER Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4999 THR Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4827 PHE Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4860 LEU Chi-restraints excluded: chain D residue 4943 LEU Chi-restraints excluded: chain E residue 4245 SER Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4984 LEU Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4172 ILE Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4472 ASN Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4835 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 340 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 chunk 566 optimal weight: 2.9990 chunk 552 optimal weight: 0.0010 chunk 4 optimal weight: 4.9990 chunk 578 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 437 optimal weight: 0.7980 chunk 388 optimal weight: 0.0000 chunk 119 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4190 GLN B4190 GLN D4188 GLN D4303 GLN E4303 GLN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4303 GLN F4414 GLN F4491 GLN ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070706 restraints weight = 91591.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.072498 restraints weight = 47897.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.073689 restraints weight = 29108.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074504 restraints weight = 19599.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075042 restraints weight = 14189.991| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 44443 Z= 0.158 Angle : 0.558 8.637 61572 Z= 0.296 Chirality : 0.045 0.182 7763 Planarity : 0.004 0.071 7980 Dihedral : 4.870 29.084 6216 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.81 % Allowed : 6.76 % Favored : 91.42 % 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 aren not related in a simple way. whole: 0.45 (0.11), residues: 5999 helix: -3.63 (0.33), residues: 84 sheet: 0.34 (0.10), residues: 2492 loop : 0.53 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F4656 TYR 0.019 0.002 TYR B4918 PHE 0.021 0.002 PHE F4264 TRP 0.017 0.002 TRP E4618 HIS 0.004 0.001 HIS F4585 Details of bonding type rmsd covalent geometry : bond 0.00365 (44373) covalent geometry : angle 0.55516 (61432) SS BOND : bond 0.00313 ( 70) SS BOND : angle 1.23227 ( 140) hydrogen bonds : bond 0.03769 ( 1288) hydrogen bonds : angle 5.35108 ( 3402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 160 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 4835 GLU cc_start: 0.8187 (tp30) cc_final: 0.7944 (tp30) REVERT: B 4246 GLU cc_start: 0.7909 (mp0) cc_final: 0.7297 (mp0) REVERT: B 4656 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8244 (ttt90) REVERT: B 4791 SER cc_start: 0.8769 (m) cc_final: 0.8411 (p) REVERT: C 4154 GLN cc_start: 0.7616 (pt0) cc_final: 0.7184 (mm110) REVERT: C 4644 LYS cc_start: 0.9215 (tttt) cc_final: 0.8961 (tttm) REVERT: D 4860 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8438 (tt) REVERT: D 4976 LEU cc_start: 0.9285 (mt) cc_final: 0.9013 (mt) REVERT: E 4432 ILE cc_start: 0.8212 (mt) cc_final: 0.7825 (tt) REVERT: E 4976 LEU cc_start: 0.9301 (mt) cc_final: 0.9052 (mt) REVERT: F 4976 LEU cc_start: 0.9094 (mt) cc_final: 0.8825 (mt) REVERT: G 4154 GLN cc_start: 0.7619 (pt0) cc_final: 0.7039 (mm110) REVERT: G 4644 LYS cc_start: 0.9161 (tttt) cc_final: 0.8641 (tttp) REVERT: G 4791 SER cc_start: 0.8887 (m) cc_final: 0.8557 (p) REVERT: G 4973 ASP cc_start: 0.8024 (t0) cc_final: 0.7700 (t0) REVERT: G 4976 LEU cc_start: 0.9174 (mt) cc_final: 0.8293 (mt) outliers start: 91 outliers final: 73 residues processed: 246 average time/residue: 0.2207 time to fit residues: 98.1766 Evaluate side-chains 216 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4547 VAL Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4860 LEU Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4943 LEU Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4999 THR Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4378 SER Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4547 VAL Chi-restraints excluded: chain C residue 4626 SER Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4827 PHE Chi-restraints excluded: chain C residue 4999 THR Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4188 GLN Chi-restraints excluded: chain D residue 4246 GLU Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4795 ILE Chi-restraints excluded: chain D residue 4827 PHE Chi-restraints excluded: chain D residue 4860 LEU Chi-restraints excluded: chain D residue 4999 THR Chi-restraints excluded: chain E residue 4228 LEU Chi-restraints excluded: chain E residue 4245 SER Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4391 VAL Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4832 MET Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4254 ILE Chi-restraints excluded: chain G residue 4270 CYS Chi-restraints excluded: chain G residue 4472 ASN Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4640 VAL Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4943 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 516 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 331 optimal weight: 1.9990 chunk 531 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 378 optimal weight: 0.0770 chunk 104 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 495 optimal weight: 3.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4986 GLN E4585 HIS E4986 GLN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4414 GLN G4509 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070880 restraints weight = 91580.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.072679 restraints weight = 47987.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073875 restraints weight = 29130.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074678 restraints weight = 19581.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075217 restraints weight = 14240.336| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44443 Z= 0.144 Angle : 0.538 8.173 61572 Z= 0.286 Chirality : 0.044 0.177 7763 Planarity : 0.004 0.070 7980 Dihedral : 4.746 37.484 6216 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 6.59 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.49 (0.11), residues: 5999 helix: -3.53 (0.35), residues: 84 sheet: 0.39 (0.10), residues: 2478 loop : 0.54 (0.11), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F4656 TYR 0.020 0.001 TYR B4918 PHE 0.022 0.001 PHE F4264 TRP 0.013 0.002 TRP E4618 HIS 0.004 0.001 HIS B4418 Details of bonding type rmsd covalent geometry : bond 0.00330 (44373) covalent geometry : angle 0.53680 (61432) SS BOND : bond 0.00130 ( 70) SS BOND : angle 1.02787 ( 140) hydrogen bonds : bond 0.03597 ( 1288) hydrogen bonds : angle 5.24879 ( 3402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 160 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4835 GLU cc_start: 0.8231 (tp30) cc_final: 0.8006 (tp30) REVERT: B 4246 GLU cc_start: 0.7903 (mp0) cc_final: 0.7290 (mp0) REVERT: B 4656 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8309 (ttt90) REVERT: B 4791 SER cc_start: 0.8853 (m) cc_final: 0.8501 (p) REVERT: C 4154 GLN cc_start: 0.7526 (pt0) cc_final: 0.7114 (mm110) REVERT: C 4644 LYS cc_start: 0.9204 (tttt) cc_final: 0.8940 (tttm) REVERT: D 4860 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8359 (tt) REVERT: E 4432 ILE cc_start: 0.8190 (mt) cc_final: 0.7830 (tt) REVERT: F 4976 LEU cc_start: 0.9127 (mt) cc_final: 0.8773 (mt) REVERT: G 4154 GLN cc_start: 0.7732 (pt0) cc_final: 0.7149 (mm110) REVERT: G 4644 LYS cc_start: 0.9170 (tttt) cc_final: 0.8704 (tttp) REVERT: G 4791 SER cc_start: 0.8904 (m) cc_final: 0.8570 (p) REVERT: G 4962 MET cc_start: 0.7728 (ptm) cc_final: 0.7491 (ttp) outliers start: 107 outliers final: 87 residues processed: 260 average time/residue: 0.2234 time to fit residues: 104.6818 Evaluate side-chains 230 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 142 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4547 VAL Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4860 LEU Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4943 LEU Chi-restraints excluded: chain B residue 4245 SER Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4410 ASP Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4460 LEU Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4547 VAL Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4962 MET Chi-restraints excluded: chain B residue 4999 THR Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4378 SER Chi-restraints excluded: chain C residue 4413 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4547 VAL Chi-restraints excluded: chain C residue 4626 SER Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4204 THR Chi-restraints excluded: chain D residue 4246 GLU Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4547 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4795 ILE Chi-restraints excluded: chain D residue 4860 LEU Chi-restraints excluded: chain D residue 4999 THR Chi-restraints excluded: chain E residue 4228 LEU Chi-restraints excluded: chain E residue 4378 SER Chi-restraints excluded: chain E residue 4413 VAL Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4265 ASN Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4391 VAL Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4832 MET Chi-restraints excluded: chain F residue 4984 LEU Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4212 TRP Chi-restraints excluded: chain G residue 4270 CYS Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4472 ASN Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4547 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4640 VAL Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4943 LEU Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 205 optimal weight: 0.6980 chunk 526 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 480 optimal weight: 2.9990 chunk 455 optimal weight: 0.1980 chunk 498 optimal weight: 1.9990 chunk 425 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 590 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4488 ASN D4188 GLN F4188 GLN F4190 GLN ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.068947 restraints weight = 92513.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.070686 restraints weight = 48595.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071851 restraints weight = 29745.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.072635 restraints weight = 20135.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.073180 restraints weight = 14726.504| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 44443 Z= 0.215 Angle : 0.592 9.161 61572 Z= 0.312 Chirality : 0.046 0.196 7763 Planarity : 0.004 0.074 7980 Dihedral : 4.917 35.634 6216 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.41 % Allowed : 7.04 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.34 (0.11), residues: 5999 helix: -3.23 (0.42), residues: 84 sheet: 0.34 (0.10), residues: 2429 loop : 0.37 (0.11), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F4656 TYR 0.021 0.002 TYR B4918 PHE 0.029 0.002 PHE F4264 TRP 0.014 0.002 TRP C4993 HIS 0.008 0.002 HIS G4418 Details of bonding type rmsd covalent geometry : bond 0.00497 (44373) covalent geometry : angle 0.59029 (61432) SS BOND : bond 0.00156 ( 70) SS BOND : angle 1.16189 ( 140) hydrogen bonds : bond 0.03987 ( 1288) hydrogen bonds : angle 5.28334 ( 3402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 149 time to evaluate : 1.595 Fit side-chains REVERT: A 4684 GLU cc_start: 0.8093 (tp30) cc_final: 0.7487 (tm-30) REVERT: B 4246 GLU cc_start: 0.7873 (mp0) cc_final: 0.7287 (mp0) REVERT: B 4656 ARG cc_start: 0.8672 (ttt-90) cc_final: 0.8363 (ttt90) REVERT: B 4791 SER cc_start: 0.8852 (m) cc_final: 0.8493 (p) REVERT: B 4860 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8375 (tt) REVERT: C 4154 GLN cc_start: 0.7417 (pt0) cc_final: 0.7098 (mm110) REVERT: C 4353 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7932 (tt0) REVERT: C 4546 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9049 (tt) REVERT: C 4644 LYS cc_start: 0.9123 (tttt) cc_final: 0.8863 (tttm) REVERT: D 4658 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7920 (mm-30) REVERT: D 4962 MET cc_start: 0.7344 (ptm) cc_final: 0.7054 (ttm) REVERT: E 4860 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8690 (tt) REVERT: E 4976 LEU cc_start: 0.9123 (mp) cc_final: 0.8797 (mt) REVERT: F 4976 LEU cc_start: 0.9123 (mt) cc_final: 0.8835 (mt) REVERT: G 4154 GLN cc_start: 0.7583 (pt0) cc_final: 0.7104 (mm110) REVERT: G 4644 LYS cc_start: 0.9119 (tttt) cc_final: 0.8737 (tttp) REVERT: G 4791 SER cc_start: 0.8904 (m) cc_final: 0.8594 (p) outliers start: 121 outliers final: 99 residues processed: 260 average time/residue: 0.2179 time to fit residues: 103.1544 Evaluate side-chains 242 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 140 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4547 VAL Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4827 PHE Chi-restraints excluded: chain A residue 4878 GLN Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4943 LEU Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4245 SER Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4318 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4410 ASP Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4460 LEU Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4547 VAL Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4827 PHE Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4962 MET Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4378 SER Chi-restraints excluded: chain C residue 4413 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4546 LEU Chi-restraints excluded: chain C residue 4547 VAL Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4827 PHE Chi-restraints excluded: chain C residue 4999 THR Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4204 THR Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4485 MET Chi-restraints excluded: chain D residue 4547 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4795 ILE Chi-restraints excluded: chain D residue 4827 PHE Chi-restraints excluded: chain D residue 4999 THR Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4245 SER Chi-restraints excluded: chain E residue 4378 SER Chi-restraints excluded: chain E residue 4413 VAL Chi-restraints excluded: chain E residue 4593 VAL Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4662 LEU Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4827 PHE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4962 MET Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4265 ASN Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4391 VAL Chi-restraints excluded: chain F residue 4413 VAL Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4547 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4827 PHE Chi-restraints excluded: chain F residue 4832 MET Chi-restraints excluded: chain F residue 4984 LEU Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4212 TRP Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4472 ASN Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4547 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4640 VAL Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4943 LEU Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 551 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 chunk 590 optimal weight: 3.9990 chunk 571 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 567 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 487 optimal weight: 2.9990 chunk 533 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4414 GLN C4414 GLN F4188 GLN ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070198 restraints weight = 92299.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.071961 restraints weight = 48416.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.073141 restraints weight = 29478.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073936 restraints weight = 19864.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.074453 restraints weight = 14449.144| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44443 Z= 0.146 Angle : 0.539 8.089 61572 Z= 0.284 Chirality : 0.044 0.183 7763 Planarity : 0.004 0.069 7980 Dihedral : 4.713 32.952 6216 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.11 % Allowed : 7.74 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.37 (0.11), residues: 5999 helix: -3.23 (0.41), residues: 84 sheet: 0.39 (0.10), residues: 2429 loop : 0.37 (0.11), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F4656 TYR 0.020 0.001 TYR F4648 PHE 0.021 0.001 PHE F4264 TRP 0.014 0.002 TRP A4618 HIS 0.003 0.001 HIS A4418 Details of bonding type rmsd covalent geometry : bond 0.00337 (44373) covalent geometry : angle 0.53777 (61432) SS BOND : bond 0.00143 ( 70) SS BOND : angle 0.96839 ( 140) hydrogen bonds : bond 0.03568 ( 1288) hydrogen bonds : angle 5.17397 ( 3402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 154 time to evaluate : 1.939 Fit side-chains REVERT: A 4460 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8685 (mt) REVERT: B 4246 GLU cc_start: 0.7843 (mp0) cc_final: 0.7244 (mp0) REVERT: B 4791 SER cc_start: 0.8856 (m) cc_final: 0.8501 (p) REVERT: B 4860 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 5002 ASN cc_start: 0.8489 (t0) cc_final: 0.8117 (m-40) REVERT: C 4154 GLN cc_start: 0.7373 (pt0) cc_final: 0.7074 (mm110) REVERT: C 4353 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7872 (tt0) REVERT: C 4546 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9012 (tt) REVERT: C 4644 LYS cc_start: 0.9106 (tttt) cc_final: 0.8839 (tttm) REVERT: D 4172 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8862 (mt) REVERT: D 4658 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7925 (mm-30) REVERT: D 4976 LEU cc_start: 0.9106 (mt) cc_final: 0.8852 (mt) REVERT: E 4860 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8634 (tt) REVERT: E 4976 LEU cc_start: 0.9133 (mp) cc_final: 0.8889 (mt) REVERT: F 4519 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8056 (ttm170) REVERT: F 4976 LEU cc_start: 0.9107 (mt) cc_final: 0.8785 (mt) REVERT: G 4154 GLN cc_start: 0.7584 (pt0) cc_final: 0.7091 (mm110) REVERT: G 4644 LYS cc_start: 0.9085 (tttt) cc_final: 0.8694 (tttp) REVERT: G 4791 SER cc_start: 0.8887 (m) cc_final: 0.8583 (p) outliers start: 106 outliers final: 89 residues processed: 253 average time/residue: 0.2294 time to fit residues: 104.7728 Evaluate side-chains 237 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 142 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4155 VAL Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4547 VAL Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4878 GLN Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4943 LEU Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4245 SER Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4318 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4460 LEU Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4547 VAL Chi-restraints excluded: chain B residue 4558 ILE Chi-restraints excluded: chain B residue 4568 ILE Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4962 MET Chi-restraints excluded: chain B residue 4999 THR Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4413 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4546 LEU Chi-restraints excluded: chain C residue 4547 VAL Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain C residue 4999 THR Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4204 THR Chi-restraints excluded: chain D residue 4246 GLU Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4547 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4593 VAL Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4795 ILE Chi-restraints excluded: chain D residue 4827 PHE Chi-restraints excluded: chain D residue 4999 THR Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4378 SER Chi-restraints excluded: chain E residue 4413 VAL Chi-restraints excluded: chain E residue 4547 VAL Chi-restraints excluded: chain E residue 4593 VAL Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4662 LEU Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4962 MET Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4265 ASN Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4345 VAL Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4519 ARG Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4547 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4212 TRP Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4517 VAL Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4547 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4640 VAL Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 327 optimal weight: 0.2980 chunk 176 optimal weight: 2.9990 chunk 533 optimal weight: 0.3980 chunk 294 optimal weight: 2.9990 chunk 483 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 403 optimal weight: 0.0770 chunk 208 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D4878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4188 GLN ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072228 restraints weight = 90934.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074022 restraints weight = 47644.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075207 restraints weight = 28881.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076006 restraints weight = 19423.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076545 restraints weight = 14102.008| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 44443 Z= 0.097 Angle : 0.512 7.813 61572 Z= 0.270 Chirality : 0.044 0.163 7763 Planarity : 0.004 0.061 7980 Dihedral : 4.446 33.792 6216 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.45 % Allowed : 8.64 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.46 (0.11), residues: 5999 helix: -3.14 (0.42), residues: 84 sheet: 0.54 (0.11), residues: 2345 loop : 0.36 (0.11), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C4656 TYR 0.021 0.001 TYR C4648 PHE 0.020 0.001 PHE F4264 TRP 0.017 0.002 TRP E4618 HIS 0.007 0.001 HIS D4418 Details of bonding type rmsd covalent geometry : bond 0.00220 (44373) covalent geometry : angle 0.50924 (61432) SS BOND : bond 0.00181 ( 70) SS BOND : angle 1.26967 ( 140) hydrogen bonds : bond 0.03130 ( 1288) hydrogen bonds : angle 5.02547 ( 3402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 157 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: B 4962 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6666 (ttm) REVERT: B 5002 ASN cc_start: 0.8520 (t0) cc_final: 0.8142 (m-40) REVERT: C 4154 GLN cc_start: 0.7413 (pt0) cc_final: 0.7098 (mm110) REVERT: C 4246 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8070 (mm-30) REVERT: C 4353 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7892 (tt0) REVERT: C 4546 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9058 (tt) REVERT: C 4644 LYS cc_start: 0.9119 (tttt) cc_final: 0.8815 (tttm) REVERT: D 4172 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8839 (mt) REVERT: D 4647 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 4658 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7997 (mm-30) REVERT: E 4860 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8565 (tt) REVERT: F 4519 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8095 (ttm170) REVERT: F 4976 LEU cc_start: 0.9081 (mt) cc_final: 0.8736 (mt) REVERT: G 4154 GLN cc_start: 0.7677 (pt0) cc_final: 0.7106 (mm110) REVERT: G 4644 LYS cc_start: 0.9141 (tttt) cc_final: 0.8806 (tttp) REVERT: G 4791 SER cc_start: 0.8881 (m) cc_final: 0.8576 (p) outliers start: 73 outliers final: 55 residues processed: 222 average time/residue: 0.2292 time to fit residues: 91.3165 Evaluate side-chains 205 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4155 VAL Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4245 SER Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4915 CYS Chi-restraints excluded: chain B residue 4962 MET Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4546 LEU Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4246 GLU Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4593 VAL Chi-restraints excluded: chain D residue 4647 LEU Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4413 VAL Chi-restraints excluded: chain E residue 4593 VAL Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4795 ILE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4962 MET Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4265 ASN Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4519 ARG Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4547 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4212 TRP Chi-restraints excluded: chain G residue 4270 CYS Chi-restraints excluded: chain G residue 4342 THR Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4517 VAL Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 341 optimal weight: 2.9990 chunk 378 optimal weight: 0.0370 chunk 495 optimal weight: 2.9990 chunk 506 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 575 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 470 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4303 GLN ** D4878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.071253 restraints weight = 92419.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073013 restraints weight = 48333.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.074192 restraints weight = 29464.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074977 restraints weight = 19881.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075490 restraints weight = 14494.675| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 44443 Z= 0.137 Angle : 0.544 17.843 61572 Z= 0.284 Chirality : 0.044 0.251 7763 Planarity : 0.004 0.063 7980 Dihedral : 4.504 34.683 6216 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.41 % Allowed : 8.95 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.46 (0.11), residues: 5999 helix: -3.03 (0.44), residues: 84 sheet: 0.56 (0.11), residues: 2331 loop : 0.33 (0.11), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B4519 TYR 0.021 0.001 TYR F4918 PHE 0.019 0.001 PHE F4264 TRP 0.013 0.002 TRP G4993 HIS 0.003 0.001 HIS B4418 Details of bonding type rmsd covalent geometry : bond 0.00317 (44373) covalent geometry : angle 0.53832 (61432) SS BOND : bond 0.00355 ( 70) SS BOND : angle 1.78909 ( 140) hydrogen bonds : bond 0.03330 ( 1288) hydrogen bonds : angle 4.96857 ( 3402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 4684 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 4860 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8607 (tt) REVERT: B 4962 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6589 (ttm) REVERT: B 5002 ASN cc_start: 0.8443 (t0) cc_final: 0.8102 (m-40) REVERT: C 4154 GLN cc_start: 0.7356 (pt0) cc_final: 0.7070 (mm110) REVERT: C 4246 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 4172 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (mt) REVERT: D 4647 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8190 (tp) REVERT: D 4658 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8000 (mm-30) REVERT: F 4976 LEU cc_start: 0.9060 (mt) cc_final: 0.8738 (mt) REVERT: G 4154 GLN cc_start: 0.7601 (pt0) cc_final: 0.7084 (mm110) REVERT: G 4644 LYS cc_start: 0.9085 (tttt) cc_final: 0.8709 (tttp) REVERT: G 4791 SER cc_start: 0.8882 (m) cc_final: 0.8597 (p) outliers start: 71 outliers final: 60 residues processed: 218 average time/residue: 0.2265 time to fit residues: 88.9032 Evaluate side-chains 206 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4155 VAL Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4432 ILE Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4943 LEU Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4254 ILE Chi-restraints excluded: chain B residue 4342 THR Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4630 SER Chi-restraints excluded: chain B residue 4640 VAL Chi-restraints excluded: chain B residue 4649 VAL Chi-restraints excluded: chain B residue 4860 LEU Chi-restraints excluded: chain B residue 4962 MET Chi-restraints excluded: chain C residue 4155 VAL Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 VAL Chi-restraints excluded: chain C residue 4795 ILE Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4246 GLU Chi-restraints excluded: chain D residue 4254 ILE Chi-restraints excluded: chain D residue 4547 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4593 VAL Chi-restraints excluded: chain D residue 4647 LEU Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4795 ILE Chi-restraints excluded: chain D residue 4999 THR Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4413 VAL Chi-restraints excluded: chain E residue 4593 VAL Chi-restraints excluded: chain E residue 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL Chi-restraints excluded: chain E residue 4962 MET Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4265 ASN Chi-restraints excluded: chain F residue 4310 ILE Chi-restraints excluded: chain F residue 4511 VAL Chi-restraints excluded: chain F residue 4523 VAL Chi-restraints excluded: chain F residue 4547 VAL Chi-restraints excluded: chain F residue 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4212 TRP Chi-restraints excluded: chain G residue 4270 CYS Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4517 VAL Chi-restraints excluded: chain G residue 4523 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4640 VAL Chi-restraints excluded: chain G residue 4649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 575 optimal weight: 3.9990 chunk 417 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 324 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 182 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 303 optimal weight: 0.0010 chunk 468 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4585 HIS C4585 HIS ** D4878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071774 restraints weight = 92335.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073556 restraints weight = 48460.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074737 restraints weight = 29483.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.075544 restraints weight = 19876.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076078 restraints weight = 14400.357| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44443 Z= 0.116 Angle : 0.525 11.711 61572 Z= 0.274 Chirality : 0.044 0.167 7763 Planarity : 0.004 0.060 7980 Dihedral : 4.410 32.936 6216 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.51 % Allowed : 9.01 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.45 (0.11), residues: 5999 helix: -2.99 (0.43), residues: 84 sheet: 0.56 (0.11), residues: 2345 loop : 0.32 (0.11), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C4656 TYR 0.021 0.001 TYR F4918 PHE 0.018 0.001 PHE F4264 TRP 0.014 0.002 TRP G4618 HIS 0.002 0.001 HIS A4418 Details of bonding type rmsd covalent geometry : bond 0.00271 (44373) covalent geometry : angle 0.52030 (61432) SS BOND : bond 0.00216 ( 70) SS BOND : angle 1.50206 ( 140) hydrogen bonds : bond 0.03187 ( 1288) hydrogen bonds : angle 4.91011 ( 3402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5931.94 seconds wall clock time: 104 minutes 34.07 seconds (6274.07 seconds total)