Starting phenix.real_space_refine on Thu Dec 26 09:01:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fly_50543/12_2024/9fly_50543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fly_50543/12_2024/9fly_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_50543/12_2024/9fly_50543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fly_50543/12_2024/9fly_50543.map" model { file = "/net/cci-nas-00/data/ceres_data/9fly_50543/12_2024/9fly_50543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fly_50543/12_2024/9fly_50543.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 23.51, per 1000 atoms: 0.54 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: 11.75 Conformation dependent library (CDL) restraints added in 6.4 seconds 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: 12.83 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: 37.80 Time building geometry restraints manager: 13.59 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 25.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 122.930 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.270 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.060 ------------------------------------------------------------------------------- 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 44373 Z= 1.189 Angle : 1.562 14.425 61432 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.029 0.007 TRP B4817 HIS 0.011 0.005 HIS G4585 PHE 0.079 0.008 PHE C4349 TYR 0.045 0.006 TYR B4227 ARG 0.008 0.002 ARG D4450 *********************** 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 : 5.241 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: 0.8599 (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: 0.7681 (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: 0.8376 (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: 0.8104 (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: 0.8414 (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: 0.7510 (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: 0.4981 time to fit residues: 451.1067 Evaluate side-chains 187 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 5.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 502 optimal weight: 0.9980 chunk 450 optimal weight: 0.0020 chunk 250 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 466 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 347 optimal weight: 0.7980 chunk 540 optimal weight: 0.5980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 A4302 ASN A4323 ASN A4509 GLN A4781 ASN ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4302 ASN B4509 GLN B4781 ASN ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4509 GLN C4781 ASN ** D4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4404 ASN D4781 ASN ** 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 F4781 ASN ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4255 ASN G4781 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 44373 Z= 0.236 Angle : 0.626 8.730 61432 Z= 0.348 Chirality : 0.048 0.163 7763 Planarity : 0.005 0.063 7980 Dihedral : 5.482 24.690 6216 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.27 % Allowed : 4.50 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 5999 helix: -3.87 (0.21), residues: 42 sheet: 0.64 (0.11), residues: 2324 loop : 0.54 (0.10), residues: 3633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B4618 HIS 0.003 0.001 HIS C4418 PHE 0.030 0.002 PHE C4954 TYR 0.017 0.002 TYR D4806 ARG 0.013 0.001 ARG G4656 *********************** 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 317 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 5.061 Fit side-chains REVERT: A 4243 CYS cc_start: 0.7745 (m) cc_final: 0.7522 (p) REVERT: A 4656 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7843 (ttt90) REVERT: A 4976 LEU cc_start: 0.9083 (mt) cc_final: 0.8817 (mt) REVERT: B 4154 GLN cc_start: 0.8106 (pt0) cc_final: 0.7788 (mm110) REVERT: B 4680 THR cc_start: 0.8133 (t) cc_final: 0.7377 (m) REVERT: B 4791 SER cc_start: 0.8772 (m) cc_final: 0.8413 (p) REVERT: C 4154 GLN cc_start: 0.7784 (pt0) cc_final: 0.7314 (mm110) REVERT: C 4172 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8411 (mm) REVERT: C 4795 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8374 (mt) REVERT: C 4976 LEU cc_start: 0.9100 (mt) cc_final: 0.8621 (mt) REVERT: D 4234 MET cc_start: 0.8669 (ttp) cc_final: 0.8207 (ttp) REVERT: D 4691 SER cc_start: 0.9299 (t) cc_final: 0.9058 (m) REVERT: D 4775 LEU cc_start: 0.8438 (mt) cc_final: 0.8102 (mt) REVERT: E 4228 LEU cc_start: 0.9026 (mt) cc_final: 0.8807 (mp) REVERT: E 4432 ILE cc_start: 0.7929 (mt) cc_final: 0.7119 (tt) REVERT: E 4483 MET cc_start: 0.8391 (ttm) cc_final: 0.7872 (ttt) REVERT: E 4791 SER cc_start: 0.8433 (m) cc_final: 0.8193 (p) REVERT: E 4976 LEU cc_start: 0.9034 (mt) cc_final: 0.8506 (mt) REVERT: F 4483 MET cc_start: 0.8132 (ttm) cc_final: 0.7909 (ttm) REVERT: F 4832 MET cc_start: 0.8159 (tmm) cc_final: 0.7654 (tmm) REVERT: F 4973 ASP cc_start: 0.7955 (t0) cc_final: 0.7650 (t0) REVERT: F 4976 LEU cc_start: 0.9057 (mt) cc_final: 0.8595 (mt) REVERT: F 5009 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6759 (mp) REVERT: G 4154 GLN cc_start: 0.7712 (pt0) cc_final: 0.7134 (mm110) REVERT: G 4455 ASP cc_start: 0.7904 (t0) cc_final: 0.7520 (t0) REVERT: G 4483 MET cc_start: 0.8346 (ttm) cc_final: 0.8105 (ttm) REVERT: G 4644 LYS cc_start: 0.9175 (tttt) cc_final: 0.8764 (ttmm) REVERT: G 4680 THR cc_start: 0.8553 (t) cc_final: 0.8049 (m) REVERT: G 4791 SER cc_start: 0.8756 (m) cc_final: 0.8440 (p) REVERT: G 4976 LEU cc_start: 0.9018 (mt) cc_final: 0.8660 (mt) outliers start: 64 outliers final: 27 residues processed: 297 average time/residue: 0.5462 time to fit residues: 290.6218 Evaluate side-chains 203 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 4.911 ------------------------------------------------------------------------------- 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 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 5009 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 300 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 367 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 541 optimal weight: 0.9990 chunk 584 optimal weight: 3.9990 chunk 482 optimal weight: 6.9990 chunk 536 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 434 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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** A4509 GLN ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4488 ASN ** B4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4509 GLN ** C4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4188 GLN ** D4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4509 GLN E4488 ASN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4488 ASN ** G4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4488 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 44373 Z= 0.400 Angle : 0.672 9.722 61432 Z= 0.363 Chirality : 0.048 0.219 7763 Planarity : 0.005 0.078 7980 Dihedral : 5.345 24.781 6216 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.17 % Allowed : 5.03 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 5999 helix: -3.82 (0.29), residues: 84 sheet: 0.48 (0.10), residues: 2345 loop : 0.41 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B4872 HIS 0.007 0.002 HIS A4418 PHE 0.021 0.002 PHE A4827 TYR 0.019 0.002 TYR B4918 ARG 0.013 0.001 ARG G4656 *********************** 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: 109 poor density : 179 time to evaluate : 5.152 Fit side-chains REVERT: A 4264 PHE cc_start: 0.8720 (m-80) cc_final: 0.8427 (m-10) REVERT: A 4976 LEU cc_start: 0.9275 (mt) cc_final: 0.9028 (mt) REVERT: B 4154 GLN cc_start: 0.7883 (pt0) cc_final: 0.7580 (mm110) REVERT: B 4246 GLU cc_start: 0.8084 (mp0) cc_final: 0.7480 (mp0) REVERT: B 4353 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8131 (tt0) REVERT: B 4391 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8762 (t) REVERT: B 4791 SER cc_start: 0.8705 (m) cc_final: 0.8336 (p) REVERT: B 4976 LEU cc_start: 0.9446 (mt) cc_final: 0.8972 (mp) REVERT: C 4154 GLN cc_start: 0.7992 (pt0) cc_final: 0.7284 (mm110) REVERT: C 4172 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8517 (mm) REVERT: C 4353 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8207 (tt0) REVERT: C 4568 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (tt) REVERT: C 4644 LYS cc_start: 0.9174 (tttt) cc_final: 0.8919 (tttm) REVERT: C 4973 ASP cc_start: 0.7768 (t0) cc_final: 0.7439 (t0) REVERT: C 4976 LEU cc_start: 0.9327 (mt) cc_final: 0.9005 (mt) REVERT: D 4775 LEU cc_start: 0.8916 (mt) cc_final: 0.8671 (mt) REVERT: E 4353 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8269 (tm-30) REVERT: E 4432 ILE cc_start: 0.8190 (mt) cc_final: 0.7580 (tt) REVERT: E 4684 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7876 (tp30) REVERT: E 4835 GLU cc_start: 0.7514 (tp30) cc_final: 0.7239 (tp30) REVERT: E 4973 ASP cc_start: 0.8041 (t0) cc_final: 0.7444 (t0) REVERT: E 4976 LEU cc_start: 0.9292 (mt) cc_final: 0.8257 (mt) REVERT: F 4483 MET cc_start: 0.8370 (ttm) cc_final: 0.7974 (ttm) REVERT: F 4835 GLU cc_start: 0.7502 (tt0) cc_final: 0.7268 (tp30) REVERT: F 4973 ASP cc_start: 0.8078 (t0) cc_final: 0.7494 (t0) REVERT: F 4976 LEU cc_start: 0.9234 (mt) cc_final: 0.8639 (mt) REVERT: G 4154 GLN cc_start: 0.7651 (pt0) cc_final: 0.6874 (mm110) REVERT: G 4455 ASP cc_start: 0.7775 (t0) cc_final: 0.7410 (t0) REVERT: G 4483 MET cc_start: 0.8271 (ttm) cc_final: 0.7582 (ttt) REVERT: G 4644 LYS cc_start: 0.9160 (tttt) cc_final: 0.8821 (tttp) REVERT: G 4791 SER cc_start: 0.8767 (m) cc_final: 0.8437 (p) REVERT: G 4973 ASP cc_start: 0.8489 (t0) cc_final: 0.8065 (t0) REVERT: G 4976 LEU cc_start: 0.9173 (mt) cc_final: 0.8396 (mt) outliers start: 109 outliers final: 74 residues processed: 279 average time/residue: 0.4798 time to fit residues: 242.1495 Evaluate side-chains 219 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 5.026 ------------------------------------------------------------------------------- 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 4342 THR Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4568 ILE Chi-restraints excluded: chain A residue 4827 PHE Chi-restraints excluded: chain A residue 4860 LEU Chi-restraints excluded: chain A residue 4878 GLN Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain A residue 4999 THR Chi-restraints excluded: chain B residue 4163 ILE 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 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 4432 ILE Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4568 ILE Chi-restraints excluded: chain C residue 4626 SER 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 C residue 4999 THR Chi-restraints excluded: chain D residue 4243 CYS 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 4827 PHE 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 4795 ILE Chi-restraints excluded: chain E residue 4827 PHE Chi-restraints excluded: chain E residue 4943 LEU Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4245 SER 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 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 534 optimal weight: 0.7980 chunk 406 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 363 optimal weight: 0.9980 chunk 543 optimal weight: 0.9990 chunk 575 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 chunk 514 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** A4488 ASN ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4190 GLN D4188 GLN D4190 GLN D4414 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44373 Z= 0.232 Angle : 0.559 9.886 61432 Z= 0.300 Chirality : 0.045 0.195 7763 Planarity : 0.004 0.073 7980 Dihedral : 4.996 23.220 6216 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.73 % Allowed : 6.15 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 5999 helix: -3.77 (0.30), residues: 84 sheet: 0.40 (0.11), residues: 2387 loop : 0.50 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E4618 HIS 0.003 0.001 HIS A4418 PHE 0.013 0.001 PHE D4815 TYR 0.017 0.002 TYR F4918 ARG 0.006 0.001 ARG D4656 *********************** 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 267 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 180 time to evaluate : 4.999 Fit side-chains revert: symmetry clash REVERT: B 4154 GLN cc_start: 0.7952 (pt0) cc_final: 0.7558 (mm-40) REVERT: B 4246 GLU cc_start: 0.8052 (mp0) cc_final: 0.7425 (mp0) REVERT: B 4791 SER cc_start: 0.8793 (m) cc_final: 0.8411 (p) REVERT: B 4973 ASP cc_start: 0.8406 (t0) cc_final: 0.8018 (t0) REVERT: B 4976 LEU cc_start: 0.9352 (mt) cc_final: 0.8773 (mp) REVERT: C 4154 GLN cc_start: 0.7985 (pt0) cc_final: 0.7287 (mm110) REVERT: C 4172 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (mm) REVERT: C 4353 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8186 (tt0) REVERT: C 4644 LYS cc_start: 0.9279 (tttt) cc_final: 0.9028 (tttm) REVERT: C 4973 ASP cc_start: 0.7545 (t0) cc_final: 0.7134 (t0) REVERT: C 4976 LEU cc_start: 0.9358 (mt) cc_final: 0.8918 (mt) REVERT: D 4234 MET cc_start: 0.8897 (ttp) cc_final: 0.8579 (tmm) REVERT: D 4519 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7760 (ttm-80) REVERT: D 4691 SER cc_start: 0.9274 (t) cc_final: 0.8965 (p) REVERT: D 4775 LEU cc_start: 0.8957 (mt) cc_final: 0.8752 (mt) REVERT: E 4432 ILE cc_start: 0.8226 (mt) cc_final: 0.7596 (tt) REVERT: E 4973 ASP cc_start: 0.7880 (t0) cc_final: 0.7228 (t0) REVERT: E 4976 LEU cc_start: 0.9304 (mt) cc_final: 0.8246 (mt) REVERT: F 4483 MET cc_start: 0.8341 (ttm) cc_final: 0.7969 (ttm) REVERT: F 4973 ASP cc_start: 0.7880 (t0) cc_final: 0.7261 (t0) REVERT: F 4976 LEU cc_start: 0.9228 (mt) cc_final: 0.8589 (mt) REVERT: G 4154 GLN cc_start: 0.7647 (pt0) cc_final: 0.6866 (mm110) REVERT: G 4353 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7830 (tt0) REVERT: G 4455 ASP cc_start: 0.7741 (t0) cc_final: 0.7393 (t0) REVERT: G 4483 MET cc_start: 0.8201 (ttm) cc_final: 0.7566 (ttt) REVERT: G 4644 LYS cc_start: 0.9197 (tttt) cc_final: 0.8652 (tttp) REVERT: G 4791 SER cc_start: 0.8948 (m) cc_final: 0.8595 (p) REVERT: G 4973 ASP cc_start: 0.8238 (t0) cc_final: 0.7845 (t0) REVERT: G 4976 LEU cc_start: 0.9202 (mt) cc_final: 0.8418 (mt) outliers start: 87 outliers final: 68 residues processed: 259 average time/residue: 0.4765 time to fit residues: 224.3227 Evaluate side-chains 225 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 4.536 ------------------------------------------------------------------------------- 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 4390 LEU Chi-restraints excluded: chain A residue 4410 ASP 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 4791 SER Chi-restraints excluded: chain A residue 4860 LEU Chi-restraints excluded: chain A residue 4887 ASN Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4517 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 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 4432 ILE 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 C residue 4860 LEU Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4378 SER Chi-restraints excluded: chain D residue 4519 ARG Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL Chi-restraints excluded: chain D residue 4827 PHE 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 4640 VAL Chi-restraints excluded: chain E residue 4649 VAL 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 4943 LEU Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4245 SER 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 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 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 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 478 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 428 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 490 optimal weight: 1.9990 chunk 397 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 516 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4190 GLN A4323 ASN ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4188 GLN D4488 ASN ** D4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4190 GLN F4188 GLN ** F4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 44373 Z= 0.578 Angle : 0.754 10.476 61432 Z= 0.401 Chirality : 0.050 0.243 7763 Planarity : 0.005 0.090 7980 Dihedral : 5.711 37.049 6216 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.79 % Allowed : 6.21 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5999 helix: -3.50 (0.39), residues: 84 sheet: 0.00 (0.10), residues: 2492 loop : 0.16 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D4817 HIS 0.012 0.003 HIS B4418 PHE 0.032 0.003 PHE G4827 TYR 0.022 0.002 TYR A4806 ARG 0.004 0.001 ARG D4656 *********************** 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 296 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 156 time to evaluate : 4.989 Fit side-chains REVERT: A 4973 ASP cc_start: 0.8148 (t0) cc_final: 0.7846 (t0) REVERT: A 4976 LEU cc_start: 0.9037 (mp) cc_final: 0.8638 (mt) REVERT: B 4154 GLN cc_start: 0.7842 (pt0) cc_final: 0.7225 (mm110) REVERT: B 4246 GLU cc_start: 0.8154 (mp0) cc_final: 0.7552 (mp0) REVERT: B 4791 SER cc_start: 0.8931 (m) cc_final: 0.8550 (p) REVERT: C 4154 GLN cc_start: 0.7884 (pt0) cc_final: 0.7195 (mm110) REVERT: C 4172 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8711 (mm) REVERT: C 4546 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9060 (tt) REVERT: C 4644 LYS cc_start: 0.9352 (tttt) cc_final: 0.9098 (tttm) REVERT: C 4973 ASP cc_start: 0.8042 (t0) cc_final: 0.7559 (t0) REVERT: C 4976 LEU cc_start: 0.9365 (mt) cc_final: 0.8824 (mt) REVERT: D 4234 MET cc_start: 0.8894 (ttp) cc_final: 0.8324 (ttp) REVERT: D 4860 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8507 (tt) REVERT: F 4483 MET cc_start: 0.8503 (ttm) cc_final: 0.8155 (ttm) REVERT: F 4973 ASP cc_start: 0.8469 (t0) cc_final: 0.7782 (t0) REVERT: F 4976 LEU cc_start: 0.9096 (mt) cc_final: 0.8558 (mt) REVERT: G 4154 GLN cc_start: 0.7939 (pt0) cc_final: 0.7150 (mm110) REVERT: G 4353 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8061 (tm-30) REVERT: G 4455 ASP cc_start: 0.7831 (t0) cc_final: 0.7625 (t0) REVERT: G 4483 MET cc_start: 0.8447 (ttm) cc_final: 0.8182 (ttt) REVERT: G 4644 LYS cc_start: 0.9267 (tttt) cc_final: 0.8684 (tttp) REVERT: G 4791 SER cc_start: 0.8815 (m) cc_final: 0.8477 (p) REVERT: G 4973 ASP cc_start: 0.8572 (t0) cc_final: 0.8120 (t0) REVERT: G 4976 LEU cc_start: 0.9157 (mt) cc_final: 0.8336 (mt) outliers start: 140 outliers final: 109 residues processed: 287 average time/residue: 0.4600 time to fit residues: 243.2418 Evaluate side-chains 251 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 139 time to evaluate : 4.157 ------------------------------------------------------------------------------- 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 4310 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4410 ASP Chi-restraints excluded: chain A residue 4413 VAL Chi-restraints excluded: chain A residue 4547 VAL 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 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 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 4385 VAL Chi-restraints excluded: chain B residue 4391 VAL 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 4485 MET 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 4718 THR Chi-restraints excluded: chain B residue 4795 ILE Chi-restraints excluded: chain B residue 4827 PHE 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 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 4568 ILE Chi-restraints excluded: chain C residue 4593 VAL Chi-restraints excluded: chain C residue 4640 VAL Chi-restraints excluded: chain C residue 4649 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 4999 THR Chi-restraints excluded: chain D residue 4155 VAL Chi-restraints excluded: chain D residue 4163 ILE 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 4547 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4649 VAL 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 D residue 4999 THR Chi-restraints excluded: chain E residue 4155 VAL Chi-restraints excluded: chain E residue 4355 ASP Chi-restraints excluded: chain E residue 4378 SER Chi-restraints excluded: chain E residue 4413 VAL 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 4649 VAL 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 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 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 4878 GLN 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 4254 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 4547 VAL Chi-restraints excluded: chain G residue 4568 ILE Chi-restraints excluded: chain G residue 4626 SER Chi-restraints excluded: chain G residue 4649 VAL Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4835 GLU Chi-restraints excluded: chain G residue 4859 THR Chi-restraints excluded: chain G residue 4943 LEU Chi-restraints excluded: chain G residue 4999 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 193 optimal weight: 0.8980 chunk 517 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 337 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 575 optimal weight: 0.8980 chunk 477 optimal weight: 1.9990 chunk 266 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4190 GLN B4414 GLN C4414 GLN D4188 GLN E4303 GLN F4190 GLN ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4414 GLN G4414 GLN G4423 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44373 Z= 0.220 Angle : 0.560 11.125 61432 Z= 0.299 Chirality : 0.045 0.192 7763 Planarity : 0.004 0.072 7980 Dihedral : 5.129 35.338 6216 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 7.72 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5999 helix: -3.48 (0.36), residues: 84 sheet: 0.05 (0.10), residues: 2492 loop : 0.32 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E4618 HIS 0.004 0.001 HIS G4418 PHE 0.019 0.001 PHE A4264 TYR 0.021 0.002 TYR F4648 ARG 0.007 0.001 ARG F4656 *********************** 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 247 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 159 time to evaluate : 5.367 Fit side-chains revert: symmetry clash REVERT: A 4460 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8867 (mt) REVERT: A 4973 ASP cc_start: 0.7803 (t0) cc_final: 0.7294 (t0) REVERT: A 4976 LEU cc_start: 0.8988 (mp) cc_final: 0.8493 (mt) REVERT: B 4154 GLN cc_start: 0.7752 (pt0) cc_final: 0.7180 (mm-40) REVERT: B 4246 GLU cc_start: 0.8110 (mp0) cc_final: 0.7463 (mp0) REVERT: B 4791 SER cc_start: 0.8928 (m) cc_final: 0.8539 (p) REVERT: B 4976 LEU cc_start: 0.9531 (mp) cc_final: 0.9077 (mp) REVERT: C 4154 GLN cc_start: 0.7832 (pt0) cc_final: 0.7191 (mm110) REVERT: C 4172 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (mm) REVERT: C 4234 MET cc_start: 0.8683 (ttp) cc_final: 0.8111 (ttp) REVERT: C 4644 LYS cc_start: 0.9323 (tttt) cc_final: 0.9057 (tttm) REVERT: C 4973 ASP cc_start: 0.7535 (t0) cc_final: 0.7055 (t0) REVERT: C 4976 LEU cc_start: 0.9349 (mt) cc_final: 0.8702 (mt) REVERT: D 4234 MET cc_start: 0.8861 (ttp) cc_final: 0.8368 (ttp) REVERT: D 4647 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8146 (tp) REVERT: D 4860 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8437 (tt) REVERT: E 4860 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8634 (tt) REVERT: E 4976 LEU cc_start: 0.9356 (mt) cc_final: 0.9006 (mt) REVERT: F 4483 MET cc_start: 0.8446 (ttm) cc_final: 0.8115 (ttm) REVERT: G 4154 GLN cc_start: 0.7899 (pt0) cc_final: 0.7144 (mm110) REVERT: G 4455 ASP cc_start: 0.7733 (t0) cc_final: 0.7497 (t0) REVERT: G 4483 MET cc_start: 0.8395 (ttm) cc_final: 0.7663 (ttt) REVERT: G 4644 LYS cc_start: 0.9207 (tttt) cc_final: 0.8754 (tttp) REVERT: G 4791 SER cc_start: 0.9046 (m) cc_final: 0.8699 (p) REVERT: G 4962 MET cc_start: 0.7857 (ptm) cc_final: 0.7635 (ttp) REVERT: G 4973 ASP cc_start: 0.8360 (t0) cc_final: 0.7886 (t0) REVERT: G 4976 LEU cc_start: 0.9220 (mt) cc_final: 0.8330 (mt) outliers start: 88 outliers final: 67 residues processed: 243 average time/residue: 0.4829 time to fit residues: 212.7301 Evaluate side-chains 212 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4460 LEU Chi-restraints excluded: chain A residue 4558 ILE Chi-restraints excluded: chain A residue 4649 VAL Chi-restraints excluded: chain A residue 4827 PHE Chi-restraints excluded: chain A residue 4887 ASN 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 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 4827 PHE 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 4172 ILE Chi-restraints excluded: chain C residue 4254 ILE Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4568 ILE 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 D residue 4155 VAL Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4345 VAL Chi-restraints excluded: chain D residue 4568 ILE Chi-restraints excluded: chain D residue 4647 LEU Chi-restraints excluded: chain D residue 4649 VAL 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 4155 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 4827 PHE Chi-restraints excluded: chain E residue 4860 LEU Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4245 SER Chi-restraints excluded: chain F residue 4254 ILE 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 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 4342 THR Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4472 ASN 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 4649 VAL Chi-restraints excluded: chain G residue 4827 PHE Chi-restraints excluded: chain G residue 4943 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 555 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 420 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 484 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 573 optimal weight: 0.6980 chunk 358 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44373 Z= 0.285 Angle : 0.569 9.902 61432 Z= 0.301 Chirality : 0.045 0.191 7763 Planarity : 0.004 0.075 7980 Dihedral : 4.999 34.452 6216 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.05 % Allowed : 7.82 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5999 helix: -3.27 (0.41), residues: 84 sheet: 0.12 (0.10), residues: 2443 loop : 0.23 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B4817 HIS 0.005 0.001 HIS B4418 PHE 0.032 0.002 PHE F4264 TYR 0.020 0.002 TYR F4648 ARG 0.005 0.001 ARG F4656 *********************** 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 252 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 149 time to evaluate : 4.750 Fit side-chains revert: symmetry clash REVERT: A 4460 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8882 (mt) REVERT: A 4976 LEU cc_start: 0.9022 (mp) cc_final: 0.8652 (mp) REVERT: B 4154 GLN cc_start: 0.7756 (pt0) cc_final: 0.7165 (mm-40) REVERT: B 4246 GLU cc_start: 0.8104 (mp0) cc_final: 0.7462 (mp0) REVERT: B 4485 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7738 (mtt) REVERT: B 4791 SER cc_start: 0.8970 (m) cc_final: 0.8584 (p) REVERT: C 4154 GLN cc_start: 0.7866 (pt0) cc_final: 0.7188 (mm110) REVERT: C 4172 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8750 (mm) REVERT: C 4234 MET cc_start: 0.8679 (ttp) cc_final: 0.8133 (ttp) REVERT: C 4353 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8221 (tt0) REVERT: C 4644 LYS cc_start: 0.9325 (tttt) cc_final: 0.9028 (tttm) REVERT: D 4234 MET cc_start: 0.8842 (ttp) cc_final: 0.8393 (ttp) REVERT: D 4647 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8190 (tp) REVERT: D 4860 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8482 (tt) REVERT: D 4962 MET cc_start: 0.7482 (ptm) cc_final: 0.7155 (ttm) REVERT: D 4973 ASP cc_start: 0.8559 (t0) cc_final: 0.8344 (t0) REVERT: D 4976 LEU cc_start: 0.9057 (mt) cc_final: 0.8605 (mt) REVERT: E 4860 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8611 (tt) REVERT: E 4976 LEU cc_start: 0.9377 (mt) cc_final: 0.9001 (mt) REVERT: F 4483 MET cc_start: 0.8462 (ttm) cc_final: 0.8129 (ttm) REVERT: F 4519 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8370 (ttm170) REVERT: F 4976 LEU cc_start: 0.9072 (mt) cc_final: 0.8738 (mt) REVERT: G 4154 GLN cc_start: 0.7929 (pt0) cc_final: 0.7133 (mm110) REVERT: G 4353 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7728 (tm-30) REVERT: G 4455 ASP cc_start: 0.7719 (t0) cc_final: 0.7497 (t0) REVERT: G 4644 LYS cc_start: 0.9236 (tttt) cc_final: 0.8745 (tttp) REVERT: G 4791 SER cc_start: 0.9065 (m) cc_final: 0.8721 (p) REVERT: G 4973 ASP cc_start: 0.8248 (t0) cc_final: 0.7801 (t0) REVERT: G 4976 LEU cc_start: 0.9128 (mt) cc_final: 0.8204 (mt) outliers start: 103 outliers final: 86 residues processed: 244 average time/residue: 0.4706 time to fit residues: 209.2273 Evaluate side-chains 231 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 138 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4254 ILE Chi-restraints excluded: chain A residue 4310 ILE Chi-restraints excluded: chain A residue 4342 THR Chi-restraints excluded: chain A residue 4390 LEU 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 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 4827 PHE Chi-restraints excluded: chain A residue 4887 ASN 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 4342 THR Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4485 MET 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 4795 ILE Chi-restraints excluded: chain B residue 4827 PHE 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 4172 ILE Chi-restraints excluded: chain C residue 4254 ILE Chi-restraints excluded: chain C residue 4332 THR Chi-restraints excluded: chain C residue 4345 VAL Chi-restraints excluded: chain C residue 4432 ILE Chi-restraints excluded: chain C residue 4523 VAL 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 4246 GLU 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 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 4827 PHE Chi-restraints excluded: chain D residue 4860 LEU 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 4310 ILE Chi-restraints excluded: chain E residue 4378 SER 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 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 4245 SER Chi-restraints excluded: chain F residue 4254 ILE 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 4519 ARG 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 G residue 4155 VAL Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4472 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 354 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 283 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 450 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44373 Z= 0.208 Angle : 0.535 7.979 61432 Z= 0.284 Chirality : 0.044 0.185 7763 Planarity : 0.004 0.068 7980 Dihedral : 4.838 32.299 6216 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.03 % Allowed : 8.30 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5999 helix: -3.23 (0.41), residues: 84 sheet: 0.18 (0.11), residues: 2394 loop : 0.26 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F4618 HIS 0.007 0.001 HIS D4418 PHE 0.019 0.001 PHE F4264 TYR 0.028 0.001 TYR C4648 ARG 0.005 0.000 ARG F4656 *********************** 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 253 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 151 time to evaluate : 5.226 Fit side-chains REVERT: A 4460 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8870 (mt) REVERT: B 4154 GLN cc_start: 0.7731 (pt0) cc_final: 0.7152 (mm-40) REVERT: B 4485 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7441 (mtt) REVERT: B 4791 SER cc_start: 0.8964 (m) cc_final: 0.8580 (p) REVERT: C 4154 GLN cc_start: 0.7853 (pt0) cc_final: 0.7181 (mm110) REVERT: C 4546 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9113 (tt) REVERT: C 4973 ASP cc_start: 0.7734 (t0) cc_final: 0.7053 (t0) REVERT: C 4976 LEU cc_start: 0.9333 (mt) cc_final: 0.8999 (mt) REVERT: D 4172 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8854 (mt) REVERT: D 4234 MET cc_start: 0.8815 (ttp) cc_final: 0.8419 (ttp) REVERT: D 4647 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8173 (tp) REVERT: D 4860 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8478 (tt) REVERT: D 4962 MET cc_start: 0.7367 (ptm) cc_final: 0.7150 (ttm) REVERT: D 4973 ASP cc_start: 0.8461 (t0) cc_final: 0.8208 (t0) REVERT: D 4976 LEU cc_start: 0.9096 (mt) cc_final: 0.8571 (mt) REVERT: E 4860 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8580 (tt) REVERT: E 4976 LEU cc_start: 0.9304 (mt) cc_final: 0.9010 (mt) REVERT: F 4483 MET cc_start: 0.8433 (ttm) cc_final: 0.8099 (ttm) REVERT: F 4519 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (ttm170) REVERT: F 4976 LEU cc_start: 0.9082 (mt) cc_final: 0.8632 (mt) REVERT: G 4154 GLN cc_start: 0.7920 (pt0) cc_final: 0.7127 (mm110) REVERT: G 4353 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7562 (tm-30) REVERT: G 4644 LYS cc_start: 0.9218 (tttt) cc_final: 0.8745 (tttp) REVERT: G 4791 SER cc_start: 0.9052 (m) cc_final: 0.8711 (p) REVERT: G 4973 ASP cc_start: 0.8112 (t0) cc_final: 0.7669 (t0) REVERT: G 4976 LEU cc_start: 0.9134 (mt) cc_final: 0.8192 (mt) outliers start: 102 outliers final: 80 residues processed: 245 average time/residue: 0.4905 time to fit residues: 217.2418 Evaluate side-chains 229 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 141 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 4887 ASN 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 4342 THR Chi-restraints excluded: chain B residue 4413 VAL Chi-restraints excluded: chain B residue 4472 ASN Chi-restraints excluded: chain B residue 4485 MET 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 4795 ILE 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 4254 ILE 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 4460 LEU Chi-restraints excluded: chain C residue 4523 VAL Chi-restraints excluded: chain C residue 4546 LEU Chi-restraints excluded: chain C residue 4568 ILE 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 4246 GLU 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 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 4860 LEU 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 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 4254 ILE 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 4519 ARG 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 4999 THR Chi-restraints excluded: chain G residue 4155 VAL 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 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 521 optimal weight: 0.3980 chunk 549 optimal weight: 3.9990 chunk 501 optimal weight: 0.0170 chunk 534 optimal weight: 0.5980 chunk 321 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 482 optimal weight: 4.9990 chunk 505 optimal weight: 1.9990 chunk 532 optimal weight: 0.6980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4303 GLN ** E4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4404 ASN ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44373 Z= 0.209 Angle : 0.532 7.913 61432 Z= 0.282 Chirality : 0.044 0.174 7763 Planarity : 0.004 0.067 7980 Dihedral : 4.726 30.906 6216 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.85 % Allowed : 8.85 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.11), residues: 5999 helix: -3.14 (0.42), residues: 84 sheet: 0.23 (0.11), residues: 2394 loop : 0.29 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G4993 HIS 0.003 0.001 HIS D4418 PHE 0.017 0.001 PHE E4264 TYR 0.023 0.001 TYR C4648 ARG 0.004 0.001 ARG F4656 *********************** 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 245 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 152 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4154 GLN cc_start: 0.7730 (pt0) cc_final: 0.7155 (mm110) REVERT: B 4791 SER cc_start: 0.8974 (m) cc_final: 0.8590 (p) REVERT: B 4962 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6886 (ttm) REVERT: C 4154 GLN cc_start: 0.7862 (pt0) cc_final: 0.7182 (mm110) REVERT: C 4353 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7975 (tt0) REVERT: C 4546 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9020 (tt) REVERT: D 4172 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8734 (mt) REVERT: D 4647 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8061 (tp) REVERT: D 4973 ASP cc_start: 0.8417 (t0) cc_final: 0.8076 (t0) REVERT: D 4976 LEU cc_start: 0.8974 (mt) cc_final: 0.8285 (mt) REVERT: E 4976 LEU cc_start: 0.9293 (mt) cc_final: 0.9015 (mt) REVERT: F 4483 MET cc_start: 0.8431 (ttm) cc_final: 0.8106 (ttm) REVERT: F 4962 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7397 (ttm) REVERT: F 4976 LEU cc_start: 0.9069 (mt) cc_final: 0.8690 (mt) REVERT: G 4154 GLN cc_start: 0.7917 (pt0) cc_final: 0.7118 (mm110) REVERT: G 4353 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7476 (tm-30) REVERT: G 4644 LYS cc_start: 0.9236 (tttt) cc_final: 0.8779 (tttp) REVERT: G 4791 SER cc_start: 0.9057 (m) cc_final: 0.8723 (p) outliers start: 93 outliers final: 81 residues processed: 236 average time/residue: 0.4724 time to fit residues: 203.4776 Evaluate side-chains 225 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 139 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4254 ILE 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 4887 ASN 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 4342 THR Chi-restraints excluded: chain B residue 4385 VAL 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 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 4795 ILE 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 4254 ILE 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 4460 LEU Chi-restraints excluded: chain C residue 4517 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 4568 ILE 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 4246 GLU 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 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 4923 VAL 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 4962 MET Chi-restraints excluded: chain E residue 4999 THR Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4245 SER Chi-restraints excluded: chain F residue 4254 ILE 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 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4656 ARG Chi-restraints excluded: chain F residue 4962 MET Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4472 ASN 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 350 optimal weight: 1.9990 chunk 565 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 392 optimal weight: 0.8980 chunk 592 optimal weight: 3.9990 chunk 545 optimal weight: 2.9990 chunk 472 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 289 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44373 Z= 0.347 Angle : 0.602 18.134 61432 Z= 0.317 Chirality : 0.046 0.198 7763 Planarity : 0.004 0.076 7980 Dihedral : 4.999 34.787 6216 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.99 % Allowed : 8.91 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 5999 helix: -3.03 (0.45), residues: 84 sheet: 0.15 (0.10), residues: 2443 loop : 0.17 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G4993 HIS 0.006 0.002 HIS B4418 PHE 0.029 0.002 PHE F4264 TYR 0.021 0.002 TYR C4648 ARG 0.004 0.001 ARG F4656 ********************** 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 244 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 144 time to evaluate : 4.990 Fit side-chains REVERT: A 4460 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8890 (mt) REVERT: B 4154 GLN cc_start: 0.7765 (pt0) cc_final: 0.7143 (mm110) REVERT: B 4482 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8807 (tp) REVERT: B 4791 SER cc_start: 0.8982 (m) cc_final: 0.8596 (p) REVERT: C 4154 GLN cc_start: 0.7897 (pt0) cc_final: 0.7177 (mm110) REVERT: C 4264 PHE cc_start: 0.8552 (m-80) cc_final: 0.8000 (m-80) REVERT: C 4546 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9100 (tt) REVERT: C 4976 LEU cc_start: 0.9356 (mt) cc_final: 0.9009 (mt) REVERT: D 4172 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8742 (mt) REVERT: D 4353 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7825 (tt0) REVERT: D 4647 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 4973 ASP cc_start: 0.8460 (t0) cc_final: 0.8121 (t0) REVERT: D 4976 LEU cc_start: 0.9006 (mt) cc_final: 0.8343 (mt) REVERT: E 4976 LEU cc_start: 0.9307 (mt) cc_final: 0.9087 (mt) REVERT: F 4483 MET cc_start: 0.8469 (ttm) cc_final: 0.8143 (ttm) REVERT: F 4976 LEU cc_start: 0.9107 (mt) cc_final: 0.8655 (mt) REVERT: G 4154 GLN cc_start: 0.7952 (pt0) cc_final: 0.7100 (mm110) REVERT: G 4353 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7744 (tm-30) REVERT: G 4644 LYS cc_start: 0.9247 (tttt) cc_final: 0.8769 (tttp) REVERT: G 4976 LEU cc_start: 0.8978 (mt) cc_final: 0.8726 (mp) outliers start: 100 outliers final: 90 residues processed: 236 average time/residue: 0.4915 time to fit residues: 210.6462 Evaluate side-chains 232 residues out of total 5026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 137 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4204 THR Chi-restraints excluded: chain A residue 4254 ILE 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 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 4827 PHE Chi-restraints excluded: chain A residue 4887 ASN 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 4342 THR Chi-restraints excluded: chain B residue 4378 SER Chi-restraints excluded: chain B residue 4385 VAL 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 4482 LEU 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 4795 ILE 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 4254 ILE 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 4460 LEU Chi-restraints excluded: chain C residue 4517 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 4568 ILE 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 4246 GLU 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 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 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 4827 PHE 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 4245 SER 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 4626 SER Chi-restraints excluded: chain F residue 4640 VAL Chi-restraints excluded: chain F residue 4649 VAL Chi-restraints excluded: chain F residue 4656 ARG Chi-restraints excluded: chain F residue 4999 THR Chi-restraints excluded: chain G residue 4155 VAL Chi-restraints excluded: chain G residue 4413 VAL Chi-restraints excluded: chain G residue 4460 LEU Chi-restraints excluded: chain G residue 4472 ASN 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 Chi-restraints excluded: chain G residue 4827 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 374 optimal weight: 3.9990 chunk 502 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 435 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 472 optimal weight: 0.0570 chunk 197 optimal weight: 0.9990 chunk 485 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4585 HIS ** A4797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4265 ASN ** 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 = 0.3141 r_free = 0.3141 target = 0.082015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.070451 restraints weight = 92401.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.072196 restraints weight = 48406.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.073351 restraints weight = 29464.766| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44373 Z= 0.187 Angle : 0.529 13.212 61432 Z= 0.279 Chirality : 0.044 0.173 7763 Planarity : 0.004 0.064 7980 Dihedral : 4.683 31.064 6216 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.67 % Allowed : 9.21 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 5999 helix: -3.06 (0.43), residues: 84 sheet: 0.23 (0.11), residues: 2394 loop : 0.21 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G4618 HIS 0.003 0.001 HIS A4418 PHE 0.022 0.001 PHE F4264 TYR 0.021 0.001 TYR C4648 ARG 0.006 0.001 ARG A4656 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6849.48 seconds wall clock time: 130 minutes 33.95 seconds (7833.95 seconds total)