Starting phenix.real_space_refine on Thu Sep 18 15:50:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flx_50542/09_2025/9flx_50542.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.137 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 77 5.16 5 C 11025 2.51 5 N 2842 2.21 5 O 3731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17675 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2525 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 26, 'TRANS': 321} Restraints were copied for chains: A, C, D, E, F, G Time building chain proxies: 2.47, per 1000 atoms: 0.14 Number of scatterers: 17675 At special positions: 0 Unit cell: (101.175, 102.24, 202.35, 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 77 16.00 O 3731 8.00 N 2842 7.00 C 11025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS B4092 " - pdb=" SG CYS B4243 " distance=2.03 Simple disulfide: pdb=" SG CYS B4173 " - pdb=" SG CYS B4325 " distance=2.05 Simple disulfide: pdb=" SG CYS B4186 " - pdb=" SG CYS B4236 " distance=2.03 Simple disulfide: pdb=" SG CYS B4270 " - pdb=" SG CYS B4406 " distance=2.04 Simple disulfide: pdb=" SG CYS A4092 " - pdb=" SG CYS A4243 " distance=2.03 Simple disulfide: pdb=" SG CYS C4092 " - pdb=" SG CYS C4243 " distance=2.03 Simple disulfide: pdb=" SG CYS D4092 " - pdb=" SG CYS D4243 " distance=2.03 Simple disulfide: pdb=" SG CYS E4092 " - pdb=" SG CYS E4243 " distance=2.03 Simple disulfide: pdb=" SG CYS F4092 " - pdb=" SG CYS F4243 " distance=2.03 Simple disulfide: pdb=" SG CYS G4092 " - pdb=" SG CYS G4243 " distance=2.03 Simple disulfide: pdb=" SG CYS A4173 " - pdb=" SG CYS A4325 " distance=2.05 Simple disulfide: pdb=" SG CYS C4173 " - pdb=" SG CYS C4325 " distance=2.05 Simple disulfide: pdb=" SG CYS D4173 " - pdb=" SG CYS D4325 " distance=2.05 Simple disulfide: pdb=" SG CYS E4173 " - pdb=" SG CYS E4325 " distance=2.05 Simple disulfide: pdb=" SG CYS F4173 " - pdb=" SG CYS F4325 " distance=2.05 Simple disulfide: pdb=" SG CYS G4173 " - pdb=" SG CYS G4325 " distance=2.05 Simple disulfide: pdb=" SG CYS A4186 " - pdb=" SG CYS A4236 " distance=2.03 Simple disulfide: pdb=" SG CYS C4186 " - pdb=" SG CYS C4236 " distance=2.03 Simple disulfide: pdb=" SG CYS D4186 " - pdb=" SG CYS D4236 " distance=2.03 Simple disulfide: pdb=" SG CYS E4186 " - pdb=" SG CYS E4236 " distance=2.03 Simple disulfide: pdb=" SG CYS F4186 " - pdb=" SG CYS F4236 " distance=2.03 Simple disulfide: pdb=" SG CYS G4186 " - pdb=" SG CYS G4236 " distance=2.03 Simple disulfide: pdb=" SG CYS A4270 " - pdb=" SG CYS A4406 " distance=2.04 Simple disulfide: pdb=" SG CYS C4270 " - pdb=" SG CYS C4406 " distance=2.04 Simple disulfide: pdb=" SG CYS D4270 " - pdb=" SG CYS D4406 " distance=2.04 Simple disulfide: pdb=" SG CYS E4270 " - pdb=" SG CYS E4406 " distance=2.04 Simple disulfide: pdb=" SG CYS F4270 " - pdb=" SG CYS F4406 " distance=2.04 Simple disulfide: pdb=" SG CYS G4270 " - pdb=" SG CYS G4406 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4466 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 84 sheets defined 3.7% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 4113 through 4115 No H-bonds generated for 'chain 'B' and resid 4113 through 4115' Processing helix chain 'B' and resid 4129 through 4133 Processing helix chain 'B' and resid 4389 through 4393 Processing helix chain 'A' and resid 4113 through 4115 No H-bonds generated for 'chain 'A' and resid 4113 through 4115' Processing helix chain 'A' and resid 4129 through 4133 Processing helix chain 'A' and resid 4389 through 4393 Processing helix chain 'C' and resid 4113 through 4115 No H-bonds generated for 'chain 'C' and resid 4113 through 4115' Processing helix chain 'C' and resid 4129 through 4133 Processing helix chain 'C' and resid 4389 through 4393 Processing helix chain 'D' and resid 4113 through 4115 No H-bonds generated for 'chain 'D' and resid 4113 through 4115' Processing helix chain 'D' and resid 4129 through 4133 Processing helix chain 'D' and resid 4389 through 4393 Processing helix chain 'E' and resid 4113 through 4115 No H-bonds generated for 'chain 'E' and resid 4113 through 4115' Processing helix chain 'E' and resid 4129 through 4133 Processing helix chain 'E' and resid 4389 through 4393 Processing helix chain 'F' and resid 4113 through 4115 No H-bonds generated for 'chain 'F' and resid 4113 through 4115' Processing helix chain 'F' and resid 4129 through 4133 Processing helix chain 'F' and resid 4389 through 4393 Processing helix chain 'G' and resid 4113 through 4115 No H-bonds generated for 'chain 'G' and resid 4113 through 4115' Processing helix chain 'G' and resid 4129 through 4133 Processing helix chain 'G' and resid 4389 through 4393 Processing sheet with id=AA1, first strand: chain 'B' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL B4091 " --> pdb=" O ASN B4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 4096 through 4097 Processing sheet with id=AA3, first strand: chain 'B' and resid 4117 through 4118 Processing sheet with id=AA4, first strand: chain 'B' and resid 4166 through 4168 Processing sheet with id=AA5, first strand: chain 'B' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4263 through 4264 Processing sheet with id=AA8, first strand: chain 'B' and resid 4273 through 4276 removed outlier: 5.888A pdb=" N GLY B4273 " --> pdb=" O ASN B4309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP B4289 " --> pdb=" O VAL B4299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP B4289 " --> pdb=" O VAL B4299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4349 through 4352 removed outlier: 6.692A pdb=" N PHE B4349 " --> pdb=" O SER B4416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS B4418 " --> pdb=" O PHE B4349 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B4351 " --> pdb=" O HIS B4418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4356 through 4357 Processing sheet with id=AB4, first strand: chain 'A' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL A4091 " --> pdb=" O ASN A4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 4096 through 4097 Processing sheet with id=AB6, first strand: chain 'A' and resid 4117 through 4118 Processing sheet with id=AB7, first strand: chain 'A' and resid 4166 through 4168 Processing sheet with id=AB8, first strand: chain 'A' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4263 through 4264 Processing sheet with id=AC2, first strand: chain 'A' and resid 4273 through 4276 removed outlier: 5.888A pdb=" N GLY A4273 " --> pdb=" O ASN A4309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP A4289 " --> pdb=" O VAL A4299 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP A4289 " --> pdb=" O VAL A4299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 4349 through 4352 removed outlier: 6.692A pdb=" N PHE A4349 " --> pdb=" O SER A4416 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A4418 " --> pdb=" O PHE A4349 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A4351 " --> pdb=" O HIS A4418 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 4356 through 4357 Processing sheet with id=AC7, first strand: chain 'C' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL C4091 " --> pdb=" O ASN C4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 4096 through 4097 Processing sheet with id=AC9, first strand: chain 'C' and resid 4117 through 4118 Processing sheet with id=AD1, first strand: chain 'C' and resid 4166 through 4168 Processing sheet with id=AD2, first strand: chain 'C' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4263 through 4264 Processing sheet with id=AD5, first strand: chain 'C' and resid 4273 through 4276 removed outlier: 5.889A pdb=" N GLY C4273 " --> pdb=" O ASN C4309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP C4289 " --> pdb=" O VAL C4299 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP C4289 " --> pdb=" O VAL C4299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 4349 through 4352 removed outlier: 6.691A pdb=" N PHE C4349 " --> pdb=" O SER C4416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS C4418 " --> pdb=" O PHE C4349 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C4351 " --> pdb=" O HIS C4418 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4356 through 4357 Processing sheet with id=AE1, first strand: chain 'D' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL D4091 " --> pdb=" O ASN D4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 4096 through 4097 Processing sheet with id=AE3, first strand: chain 'D' and resid 4117 through 4118 Processing sheet with id=AE4, first strand: chain 'D' and resid 4166 through 4168 Processing sheet with id=AE5, first strand: chain 'D' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 4171 through 4173 removed outlier: 7.064A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4263 through 4264 Processing sheet with id=AE8, first strand: chain 'D' and resid 4273 through 4276 removed outlier: 5.888A pdb=" N GLY D4273 " --> pdb=" O ASN D4309 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP D4289 " --> pdb=" O VAL D4299 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP D4289 " --> pdb=" O VAL D4299 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 4349 through 4352 removed outlier: 6.691A pdb=" N PHE D4349 " --> pdb=" O SER D4416 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS D4418 " --> pdb=" O PHE D4349 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL D4351 " --> pdb=" O HIS D4418 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 4356 through 4357 Processing sheet with id=AF4, first strand: chain 'E' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL E4091 " --> pdb=" O ASN E4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 4096 through 4097 Processing sheet with id=AF6, first strand: chain 'E' and resid 4117 through 4118 Processing sheet with id=AF7, first strand: chain 'E' and resid 4166 through 4168 Processing sheet with id=AF8, first strand: chain 'E' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 4263 through 4264 Processing sheet with id=AG2, first strand: chain 'E' and resid 4273 through 4276 removed outlier: 5.889A pdb=" N GLY E4273 " --> pdb=" O ASN E4309 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP E4289 " --> pdb=" O VAL E4299 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 4298 through 4300 removed outlier: 6.669A pdb=" N TRP E4289 " --> pdb=" O VAL E4299 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 4349 through 4352 removed outlier: 6.691A pdb=" N PHE E4349 " --> pdb=" O SER E4416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS E4418 " --> pdb=" O PHE E4349 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL E4351 " --> pdb=" O HIS E4418 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 4356 through 4357 Processing sheet with id=AG7, first strand: chain 'F' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL F4091 " --> pdb=" O ASN F4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'F' and resid 4096 through 4097 Processing sheet with id=AG9, first strand: chain 'F' and resid 4117 through 4118 Processing sheet with id=AH1, first strand: chain 'F' and resid 4166 through 4168 Processing sheet with id=AH2, first strand: chain 'F' and resid 4171 through 4173 removed outlier: 7.063A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4171 through 4173 removed outlier: 7.063A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 4263 through 4264 Processing sheet with id=AH5, first strand: chain 'F' and resid 4273 through 4276 removed outlier: 5.889A pdb=" N GLY F4273 " --> pdb=" O ASN F4309 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP F4289 " --> pdb=" O VAL F4299 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP F4289 " --> pdb=" O VAL F4299 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 4349 through 4352 removed outlier: 6.691A pdb=" N PHE F4349 " --> pdb=" O SER F4416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS F4418 " --> pdb=" O PHE F4349 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL F4351 " --> pdb=" O HIS F4418 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 4356 through 4357 Processing sheet with id=AI1, first strand: chain 'G' and resid 4091 through 4092 removed outlier: 6.804A pdb=" N VAL G4091 " --> pdb=" O ASN G4158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'G' and resid 4096 through 4097 Processing sheet with id=AI3, first strand: chain 'G' and resid 4117 through 4118 Processing sheet with id=AI4, first strand: chain 'G' and resid 4166 through 4168 Processing sheet with id=AI5, first strand: chain 'G' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 4171 through 4173 removed outlier: 7.065A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 4263 through 4264 Processing sheet with id=AI8, first strand: chain 'G' and resid 4273 through 4276 removed outlier: 5.889A pdb=" N GLY G4273 " --> pdb=" O ASN G4309 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP G4289 " --> pdb=" O VAL G4299 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 4298 through 4300 removed outlier: 6.670A pdb=" N TRP G4289 " --> pdb=" O VAL G4299 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 4349 through 4352 removed outlier: 6.691A pdb=" N PHE G4349 " --> pdb=" O SER G4416 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS G4418 " --> pdb=" O PHE G4349 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL G4351 " --> pdb=" O HIS G4418 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 4356 through 4357 567 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4643 1.33 - 1.45: 4282 1.45 - 1.57: 9079 1.57 - 1.70: 21 1.70 - 1.82: 84 Bond restraints: 18109 Sorted by residual: bond pdb=" CA SER C4135 " pdb=" CB SER C4135 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" CA SER F4135 " pdb=" CB SER F4135 " ideal model delta sigma weight residual 1.527 1.477 0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" CA SER B4135 " pdb=" CB SER B4135 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" CA SER E4135 " pdb=" CB SER E4135 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" CA SER G4135 " pdb=" CB SER G4135 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.30e-02 5.92e+03 1.49e+01 ... (remaining 18104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 22435 2.36 - 4.71: 2340 4.71 - 7.07: 257 7.07 - 9.43: 42 9.43 - 11.78: 21 Bond angle restraints: 25095 Sorted by residual: angle pdb=" C GLY D4372 " pdb=" N PRO D4373 " pdb=" CA PRO D4373 " ideal model delta sigma weight residual 119.32 127.50 -8.18 1.14e+00 7.69e-01 5.15e+01 angle pdb=" C GLY F4372 " pdb=" N PRO F4373 " pdb=" CA PRO F4373 " ideal model delta sigma weight residual 119.32 127.49 -8.17 1.14e+00 7.69e-01 5.13e+01 angle pdb=" C GLY G4372 " pdb=" N PRO G4373 " pdb=" CA PRO G4373 " ideal model delta sigma weight residual 119.32 127.48 -8.16 1.14e+00 7.69e-01 5.12e+01 angle pdb=" C GLY B4372 " pdb=" N PRO B4373 " pdb=" CA PRO B4373 " ideal model delta sigma weight residual 119.32 127.46 -8.14 1.14e+00 7.69e-01 5.09e+01 angle pdb=" C GLY E4372 " pdb=" N PRO E4373 " pdb=" CA PRO E4373 " ideal model delta sigma weight residual 119.32 127.45 -8.13 1.14e+00 7.69e-01 5.09e+01 ... (remaining 25090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 9968 13.63 - 27.26: 469 27.26 - 40.89: 63 40.89 - 54.52: 42 54.52 - 68.15: 28 Dihedral angle restraints: 10570 sinusoidal: 3591 harmonic: 6979 Sorted by residual: dihedral pdb=" CB CYS D4186 " pdb=" SG CYS D4186 " pdb=" SG CYS D4236 " pdb=" CB CYS D4236 " ideal model delta sinusoidal sigma weight residual 93.00 37.13 55.87 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS F4186 " pdb=" SG CYS F4186 " pdb=" SG CYS F4236 " pdb=" CB CYS F4236 " ideal model delta sinusoidal sigma weight residual 93.00 37.15 55.85 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS G4186 " pdb=" SG CYS G4186 " pdb=" SG CYS G4236 " pdb=" CB CYS G4236 " ideal model delta sinusoidal sigma weight residual 93.00 37.15 55.85 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 10567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1892 0.064 - 0.127: 942 0.127 - 0.191: 239 0.191 - 0.255: 13 0.255 - 0.318: 29 Chirality restraints: 3115 Sorted by residual: chirality pdb=" CB VAL F4140 " pdb=" CA VAL F4140 " pdb=" CG1 VAL F4140 " pdb=" CG2 VAL F4140 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB VAL D4140 " pdb=" CA VAL D4140 " pdb=" CG1 VAL D4140 " pdb=" CG2 VAL D4140 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL A4140 " pdb=" CA VAL A4140 " pdb=" CG1 VAL A4140 " pdb=" CG2 VAL A4140 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3112 not shown) Planarity restraints: 3255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C4227 " 0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR C4227 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C4227 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C4227 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C4227 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR C4227 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C4227 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C4227 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D4227 " 0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR D4227 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR D4227 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D4227 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR D4227 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D4227 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR D4227 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D4227 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F4227 " -0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR F4227 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR F4227 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F4227 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F4227 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR F4227 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F4227 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F4227 " -0.033 2.00e-02 2.50e+03 ... (remaining 3252 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 817 2.68 - 3.24: 17033 3.24 - 3.79: 28369 3.79 - 4.35: 35524 4.35 - 4.90: 58206 Nonbonded interactions: 139949 Sorted by model distance: nonbonded pdb=" OG SER E4183 " pdb=" OG SER F4198 " model vdw 2.126 3.040 nonbonded pdb=" OG SER C4183 " pdb=" OG SER D4198 " model vdw 2.145 3.040 nonbonded pdb=" OG SER F4183 " pdb=" OG SER G4198 " model vdw 2.150 3.040 nonbonded pdb=" OG SER D4183 " pdb=" OG SER E4198 " model vdw 2.151 3.040 nonbonded pdb=" OG SER B4183 " pdb=" OG SER A4198 " model vdw 2.156 3.040 ... (remaining 139944 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 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 : 0.017 0.087 18137 Z= 0.873 Angle : 1.523 11.783 25151 Z= 1.004 Chirality : 0.078 0.318 3115 Planarity : 0.008 0.028 3255 Dihedral : 9.300 68.146 6020 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2422 helix: -2.03 (0.93), residues: 42 sheet: -0.24 (0.16), residues: 910 loop : 0.91 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F4075 TYR 0.046 0.008 TYR A4233 PHE 0.051 0.007 PHE F4399 TRP 0.030 0.005 TRP C4370 HIS 0.009 0.003 HIS C4137 Details of bonding type rmsd covalent geometry : bond 0.01733 (18109) covalent geometry : angle 1.51831 (25095) SS BOND : bond 0.01235 ( 28) SS BOND : angle 3.06430 ( 56) hydrogen bonds : bond 0.19082 ( 490) hydrogen bonds : angle 8.21309 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: B 4154 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7821 (tt0) REVERT: B 4165 THR cc_start: 0.8203 (m) cc_final: 0.7967 (t) REVERT: B 4176 ASP cc_start: 0.7709 (m-30) cc_final: 0.7391 (m-30) REVERT: B 4216 SER cc_start: 0.8297 (m) cc_final: 0.7780 (p) REVERT: B 4259 SER cc_start: 0.7101 (p) cc_final: 0.6872 (m) REVERT: B 4278 SER cc_start: 0.8060 (p) cc_final: 0.7827 (t) REVERT: B 4308 SER cc_start: 0.8145 (p) cc_final: 0.7918 (m) REVERT: B 4402 ASP cc_start: 0.7294 (t0) cc_final: 0.6932 (m-30) REVERT: A 4216 SER cc_start: 0.8260 (m) cc_final: 0.7783 (p) REVERT: A 4278 SER cc_start: 0.8168 (p) cc_final: 0.7927 (t) REVERT: C 4154 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7631 (tt0) REVERT: C 4216 SER cc_start: 0.8113 (m) cc_final: 0.7676 (p) REVERT: C 4278 SER cc_start: 0.8244 (p) cc_final: 0.8024 (t) REVERT: C 4302 ASN cc_start: 0.7446 (m-40) cc_final: 0.7058 (t0) REVERT: D 4147 GLN cc_start: 0.7905 (mt0) cc_final: 0.7625 (mt0) REVERT: D 4278 SER cc_start: 0.8171 (p) cc_final: 0.7925 (t) REVERT: D 4302 ASN cc_start: 0.7722 (m-40) cc_final: 0.7269 (t0) REVERT: D 4368 TYR cc_start: 0.7756 (m-80) cc_final: 0.7430 (m-80) REVERT: D 4379 ASN cc_start: 0.7796 (p0) cc_final: 0.7579 (p0) REVERT: E 4216 SER cc_start: 0.8163 (m) cc_final: 0.7596 (p) REVERT: E 4278 SER cc_start: 0.8240 (p) cc_final: 0.7894 (t) REVERT: E 4302 ASN cc_start: 0.7435 (m-40) cc_final: 0.6966 (t0) REVERT: E 4379 ASN cc_start: 0.7566 (p0) cc_final: 0.7237 (p0) REVERT: F 4165 THR cc_start: 0.7847 (m) cc_final: 0.7625 (t) REVERT: F 4216 SER cc_start: 0.8384 (m) cc_final: 0.7735 (p) REVERT: F 4259 SER cc_start: 0.7057 (p) cc_final: 0.6812 (m) REVERT: F 4278 SER cc_start: 0.8136 (p) cc_final: 0.7825 (t) REVERT: F 4302 ASN cc_start: 0.7278 (m-40) cc_final: 0.6830 (t0) REVERT: F 4304 ASN cc_start: 0.7007 (m-40) cc_final: 0.6780 (m-40) REVERT: F 4379 ASN cc_start: 0.7547 (p0) cc_final: 0.7162 (p0) REVERT: F 4402 ASP cc_start: 0.7208 (t0) cc_final: 0.6629 (m-30) REVERT: G 4165 THR cc_start: 0.8213 (m) cc_final: 0.7993 (t) REVERT: G 4216 SER cc_start: 0.8566 (m) cc_final: 0.7999 (p) REVERT: G 4259 SER cc_start: 0.7170 (p) cc_final: 0.6951 (m) REVERT: G 4278 SER cc_start: 0.8100 (p) cc_final: 0.7855 (t) REVERT: G 4308 SER cc_start: 0.8066 (p) cc_final: 0.7813 (m) REVERT: G 4410 ASP cc_start: 0.8596 (p0) cc_final: 0.8331 (p0) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.0988 time to fit residues: 89.1521 Evaluate side-chains 260 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4147 GLN B4185 ASN B4414 GLN A4147 GLN C4414 GLN D4147 GLN E4147 GLN E4414 GLN F4147 GLN F4414 GLN G4414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118457 restraints weight = 21076.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121059 restraints weight = 11983.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122830 restraints weight = 7857.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124017 restraints weight = 5737.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124739 restraints weight = 4527.834| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18137 Z= 0.141 Angle : 0.609 6.344 25151 Z= 0.338 Chirality : 0.047 0.154 3115 Planarity : 0.005 0.054 3255 Dihedral : 5.285 18.957 2527 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.12 % Allowed : 10.87 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.16), residues: 2422 helix: -2.93 (0.60), residues: 42 sheet: 0.22 (0.16), residues: 875 loop : 0.74 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G4075 TYR 0.019 0.001 TYR D4233 PHE 0.017 0.002 PHE G4399 TRP 0.016 0.002 TRP C4370 HIS 0.003 0.001 HIS F4137 Details of bonding type rmsd covalent geometry : bond 0.00327 (18109) covalent geometry : angle 0.60156 (25095) SS BOND : bond 0.00641 ( 28) SS BOND : angle 2.05181 ( 56) hydrogen bonds : bond 0.03837 ( 490) hydrogen bonds : angle 5.94584 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 318 time to evaluate : 0.627 Fit side-chains REVERT: B 4165 THR cc_start: 0.8355 (m) cc_final: 0.7858 (p) REVERT: B 4259 SER cc_start: 0.8106 (p) cc_final: 0.7786 (m) REVERT: B 4278 SER cc_start: 0.8977 (p) cc_final: 0.8652 (t) REVERT: A 4379 ASN cc_start: 0.8427 (p0) cc_final: 0.7859 (p0) REVERT: A 4402 ASP cc_start: 0.8017 (t0) cc_final: 0.7790 (m-30) REVERT: C 4216 SER cc_start: 0.8501 (m) cc_final: 0.8122 (p) REVERT: D 4176 ASP cc_start: 0.7685 (m-30) cc_final: 0.7355 (m-30) REVERT: D 4278 SER cc_start: 0.8960 (p) cc_final: 0.8741 (t) REVERT: D 4368 TYR cc_start: 0.9002 (m-80) cc_final: 0.8802 (m-80) REVERT: D 4379 ASN cc_start: 0.8572 (p0) cc_final: 0.8200 (p0) REVERT: E 4379 ASN cc_start: 0.8405 (p0) cc_final: 0.7911 (p0) REVERT: F 4147 GLN cc_start: 0.8659 (mt0) cc_final: 0.8357 (mt0) REVERT: F 4165 THR cc_start: 0.8180 (m) cc_final: 0.7936 (p) REVERT: F 4216 SER cc_start: 0.8682 (m) cc_final: 0.8168 (p) REVERT: F 4259 SER cc_start: 0.7978 (p) cc_final: 0.7652 (m) REVERT: F 4402 ASP cc_start: 0.7808 (t0) cc_final: 0.7529 (m-30) REVERT: G 4147 GLN cc_start: 0.8683 (mt0) cc_final: 0.8383 (mt0) REVERT: G 4216 SER cc_start: 0.8737 (m) cc_final: 0.8289 (p) REVERT: G 4259 SER cc_start: 0.8149 (p) cc_final: 0.7842 (m) REVERT: G 4379 ASN cc_start: 0.8513 (p0) cc_final: 0.8077 (p0) outliers start: 64 outliers final: 36 residues processed: 358 average time/residue: 0.1018 time to fit residues: 62.2095 Evaluate side-chains 243 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4075 ARG Chi-restraints excluded: chain B residue 4107 SER Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4397 THR Chi-restraints excluded: chain A residue 4075 ARG Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4311 THR Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4075 ARG Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4239 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4397 THR Chi-restraints excluded: chain D residue 4099 LEU Chi-restraints excluded: chain D residue 4107 SER Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4239 THR Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4311 THR Chi-restraints excluded: chain E residue 4107 SER Chi-restraints excluded: chain E residue 4130 LEU Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4075 ARG Chi-restraints excluded: chain F residue 4076 ILE Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4257 ILE Chi-restraints excluded: chain F residue 4311 THR Chi-restraints excluded: chain G residue 4106 THR Chi-restraints excluded: chain G residue 4167 THR Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 223 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4142 ASN B4185 ASN ** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4142 ASN E4142 ASN F4142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.105245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.087182 restraints weight = 22915.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.089052 restraints weight = 15021.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.090436 restraints weight = 10851.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.091459 restraints weight = 8490.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.092162 restraints weight = 7044.760| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 18137 Z= 0.315 Angle : 0.723 6.956 25151 Z= 0.394 Chirality : 0.053 0.214 3115 Planarity : 0.006 0.056 3255 Dihedral : 5.825 24.224 2527 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.31 % Allowed : 11.31 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2422 helix: -3.52 (0.44), residues: 42 sheet: -0.29 (0.16), residues: 931 loop : 0.46 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D4075 TYR 0.015 0.002 TYR F4139 PHE 0.015 0.002 PHE C4399 TRP 0.017 0.002 TRP F4232 HIS 0.006 0.002 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00778 (18109) covalent geometry : angle 0.71586 (25095) SS BOND : bond 0.00492 ( 28) SS BOND : angle 2.28980 ( 56) hydrogen bonds : bond 0.04690 ( 490) hydrogen bonds : angle 5.77811 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 236 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 4259 SER cc_start: 0.8254 (p) cc_final: 0.7852 (m) REVERT: A 4368 TYR cc_start: 0.9143 (m-80) cc_final: 0.8746 (m-80) REVERT: A 4379 ASN cc_start: 0.8805 (p0) cc_final: 0.8306 (p0) REVERT: C 4154 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7606 (tt0) REVERT: C 4216 SER cc_start: 0.8680 (m) cc_final: 0.8238 (p) REVERT: C 4311 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8999 (t) REVERT: C 4368 TYR cc_start: 0.9093 (m-80) cc_final: 0.8719 (m-80) REVERT: D 4104 ASN cc_start: 0.8463 (m-40) cc_final: 0.8226 (m-40) REVERT: D 4176 ASP cc_start: 0.7847 (m-30) cc_final: 0.7544 (m-30) REVERT: D 4185 ASN cc_start: 0.8620 (p0) cc_final: 0.8413 (p0) REVERT: D 4379 ASN cc_start: 0.8951 (p0) cc_final: 0.8232 (p0) REVERT: E 4379 ASN cc_start: 0.8850 (p0) cc_final: 0.8418 (p0) REVERT: F 4259 SER cc_start: 0.8113 (p) cc_final: 0.7731 (m) REVERT: F 4368 TYR cc_start: 0.9150 (m-80) cc_final: 0.8735 (m-80) REVERT: G 4147 GLN cc_start: 0.8782 (mt0) cc_final: 0.8472 (mt0) REVERT: G 4216 SER cc_start: 0.8865 (m) cc_final: 0.8408 (p) REVERT: G 4259 SER cc_start: 0.8197 (p) cc_final: 0.7886 (m) REVERT: G 4379 ASN cc_start: 0.8829 (p0) cc_final: 0.8421 (p0) outliers start: 109 outliers final: 81 residues processed: 318 average time/residue: 0.1033 time to fit residues: 56.1161 Evaluate side-chains 273 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 191 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4100 THR Chi-restraints excluded: chain B residue 4101 THR Chi-restraints excluded: chain B residue 4107 SER Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4179 THR Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4260 THR Chi-restraints excluded: chain B residue 4306 THR Chi-restraints excluded: chain B residue 4311 THR Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain B residue 4400 ILE Chi-restraints excluded: chain A residue 4100 THR Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4179 THR Chi-restraints excluded: chain A residue 4210 VAL Chi-restraints excluded: chain A residue 4240 ILE Chi-restraints excluded: chain A residue 4271 ILE Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4311 THR Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4239 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4308 SER Chi-restraints excluded: chain C residue 4311 THR Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain C residue 4397 THR Chi-restraints excluded: chain C residue 4404 ASN Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4179 THR Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4260 THR Chi-restraints excluded: chain D residue 4271 ILE Chi-restraints excluded: chain D residue 4306 THR Chi-restraints excluded: chain D residue 4308 SER Chi-restraints excluded: chain D residue 4311 THR Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain D residue 4404 ASN Chi-restraints excluded: chain E residue 4075 ARG Chi-restraints excluded: chain E residue 4101 THR Chi-restraints excluded: chain E residue 4107 SER Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4179 THR Chi-restraints excluded: chain E residue 4210 VAL Chi-restraints excluded: chain E residue 4240 ILE Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4271 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4306 THR Chi-restraints excluded: chain E residue 4308 SER Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4099 LEU Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4210 VAL Chi-restraints excluded: chain F residue 4234 MET Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4257 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain F residue 4306 THR Chi-restraints excluded: chain F residue 4308 SER Chi-restraints excluded: chain F residue 4311 THR Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain F residue 4397 THR Chi-restraints excluded: chain G residue 4101 THR Chi-restraints excluded: chain G residue 4106 THR Chi-restraints excluded: chain G residue 4107 SER Chi-restraints excluded: chain G residue 4210 VAL Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4302 ASN Chi-restraints excluded: chain G residue 4306 THR Chi-restraints excluded: chain G residue 4311 THR Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 136 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 216 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112145 restraints weight = 21442.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114580 restraints weight = 12241.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116301 restraints weight = 8069.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117390 restraints weight = 5890.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118154 restraints weight = 4695.777| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18137 Z= 0.120 Angle : 0.551 6.616 25151 Z= 0.294 Chirality : 0.046 0.166 3115 Planarity : 0.005 0.052 3255 Dihedral : 5.080 20.970 2527 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.46 % Allowed : 13.75 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2422 helix: -3.66 (0.39), residues: 42 sheet: 0.08 (0.17), residues: 847 loop : 0.44 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A4244 TYR 0.015 0.001 TYR A4139 PHE 0.019 0.001 PHE E4399 TRP 0.013 0.001 TRP C4370 HIS 0.003 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00293 (18109) covalent geometry : angle 0.54887 (25095) SS BOND : bond 0.00101 ( 28) SS BOND : angle 1.20189 ( 56) hydrogen bonds : bond 0.03217 ( 490) hydrogen bonds : angle 5.37136 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 256 time to evaluate : 0.714 Fit side-chains REVERT: B 4259 SER cc_start: 0.8122 (p) cc_final: 0.7722 (m) REVERT: B 4278 SER cc_start: 0.9373 (p) cc_final: 0.8885 (t) REVERT: A 4368 TYR cc_start: 0.9031 (m-80) cc_final: 0.8480 (m-80) REVERT: A 4379 ASN cc_start: 0.8807 (p0) cc_final: 0.8324 (p0) REVERT: C 4154 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7562 (tt0) REVERT: D 4104 ASN cc_start: 0.8449 (m-40) cc_final: 0.8211 (m-40) REVERT: D 4117 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8301 (tm-30) REVERT: D 4176 ASP cc_start: 0.7641 (m-30) cc_final: 0.7352 (m-30) REVERT: D 4185 ASN cc_start: 0.8594 (p0) cc_final: 0.8336 (p0) REVERT: D 4308 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8491 (p) REVERT: E 4379 ASN cc_start: 0.8805 (p0) cc_final: 0.8413 (p0) REVERT: F 4117 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 4216 SER cc_start: 0.8807 (m) cc_final: 0.8242 (p) REVERT: F 4259 SER cc_start: 0.7981 (p) cc_final: 0.7596 (m) REVERT: F 4308 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8543 (p) REVERT: G 4216 SER cc_start: 0.8769 (m) cc_final: 0.8292 (p) REVERT: G 4259 SER cc_start: 0.8069 (p) cc_final: 0.7764 (m) REVERT: G 4379 ASN cc_start: 0.8853 (p0) cc_final: 0.8426 (p0) outliers start: 71 outliers final: 41 residues processed: 305 average time/residue: 0.1066 time to fit residues: 55.5631 Evaluate side-chains 234 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4107 SER Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4271 ILE Chi-restraints excluded: chain B residue 4308 SER Chi-restraints excluded: chain B residue 4364 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain A residue 4082 THR Chi-restraints excluded: chain A residue 4240 ILE Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4364 VAL Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4107 SER Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4271 ILE Chi-restraints excluded: chain D residue 4308 SER Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4240 ILE Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4271 ILE Chi-restraints excluded: chain E residue 4308 SER Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4308 SER Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4271 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4371 THR Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 212 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111272 restraints weight = 21428.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.112361 restraints weight = 14869.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112802 restraints weight = 11831.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.113240 restraints weight = 9641.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114698 restraints weight = 8362.748| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18137 Z= 0.182 Angle : 0.581 6.762 25151 Z= 0.309 Chirality : 0.047 0.166 3115 Planarity : 0.005 0.055 3255 Dihedral : 5.118 20.001 2527 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.90 % Allowed : 14.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2422 helix: -3.90 (0.32), residues: 42 sheet: -0.31 (0.16), residues: 903 loop : 0.55 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A4244 TYR 0.017 0.001 TYR F4139 PHE 0.018 0.002 PHE B4399 TRP 0.011 0.002 TRP A4370 HIS 0.003 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00448 (18109) covalent geometry : angle 0.57775 (25095) SS BOND : bond 0.00146 ( 28) SS BOND : angle 1.41636 ( 56) hydrogen bonds : bond 0.03684 ( 490) hydrogen bonds : angle 5.35444 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.676 Fit side-chains REVERT: B 4259 SER cc_start: 0.8208 (p) cc_final: 0.7778 (m) REVERT: B 4278 SER cc_start: 0.9435 (p) cc_final: 0.8926 (t) REVERT: A 4368 TYR cc_start: 0.9052 (m-80) cc_final: 0.8577 (m-80) REVERT: A 4379 ASN cc_start: 0.8886 (p0) cc_final: 0.8420 (p0) REVERT: C 4154 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7530 (tt0) REVERT: D 4104 ASN cc_start: 0.8462 (m-40) cc_final: 0.8236 (m-40) REVERT: D 4185 ASN cc_start: 0.8551 (p0) cc_final: 0.8326 (p0) REVERT: D 4308 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 4379 ASN cc_start: 0.8876 (p0) cc_final: 0.8505 (p0) REVERT: F 4117 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 4259 SER cc_start: 0.8050 (p) cc_final: 0.7631 (m) REVERT: F 4308 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8540 (p) REVERT: G 4216 SER cc_start: 0.8823 (m) cc_final: 0.8391 (p) REVERT: G 4259 SER cc_start: 0.8198 (p) cc_final: 0.7823 (m) REVERT: G 4379 ASN cc_start: 0.8864 (p0) cc_final: 0.8433 (p0) outliers start: 80 outliers final: 60 residues processed: 268 average time/residue: 0.1060 time to fit residues: 48.1133 Evaluate side-chains 245 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4101 THR Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4271 ILE Chi-restraints excluded: chain B residue 4308 SER Chi-restraints excluded: chain B residue 4311 THR Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain B residue 4391 VAL Chi-restraints excluded: chain A residue 4082 THR Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4101 THR Chi-restraints excluded: chain D residue 4107 SER Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4278 SER Chi-restraints excluded: chain D residue 4308 SER Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4210 VAL Chi-restraints excluded: chain E residue 4240 ILE Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4271 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4308 SER Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4179 THR Chi-restraints excluded: chain F residue 4210 VAL Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4257 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain F residue 4308 SER Chi-restraints excluded: chain F residue 4339 VAL Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4107 SER Chi-restraints excluded: chain G residue 4210 VAL Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4371 THR Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 209 optimal weight: 0.0980 chunk 149 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4142 ASN D4142 ASN E4142 ASN F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098800 restraints weight = 21998.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100575 restraints weight = 14336.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.101878 restraints weight = 10348.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102773 restraints weight = 8184.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.103255 restraints weight = 6871.966| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18137 Z= 0.089 Angle : 0.500 6.778 25151 Z= 0.262 Chirality : 0.044 0.163 3115 Planarity : 0.005 0.047 3255 Dihedral : 4.491 20.401 2527 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.19 % Allowed : 16.67 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2422 helix: -3.77 (0.35), residues: 42 sheet: -0.15 (0.16), residues: 980 loop : 0.60 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C4244 TYR 0.012 0.001 TYR D4233 PHE 0.019 0.001 PHE E4399 TRP 0.014 0.001 TRP E4370 HIS 0.002 0.001 HIS D4137 Details of bonding type rmsd covalent geometry : bond 0.00210 (18109) covalent geometry : angle 0.49967 (25095) SS BOND : bond 0.00129 ( 28) SS BOND : angle 0.74689 ( 56) hydrogen bonds : bond 0.02738 ( 490) hydrogen bonds : angle 5.00296 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.590 Fit side-chains REVERT: B 4259 SER cc_start: 0.8053 (p) cc_final: 0.7619 (m) REVERT: B 4278 SER cc_start: 0.9339 (p) cc_final: 0.8900 (t) REVERT: A 4368 TYR cc_start: 0.8963 (m-80) cc_final: 0.8416 (m-80) REVERT: C 4154 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7571 (tt0) REVERT: D 4104 ASN cc_start: 0.8442 (m-40) cc_final: 0.8240 (m-40) REVERT: E 4379 ASN cc_start: 0.8829 (p0) cc_final: 0.8438 (p0) REVERT: F 4117 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8288 (tm-30) REVERT: F 4259 SER cc_start: 0.7875 (p) cc_final: 0.7484 (m) REVERT: G 4216 SER cc_start: 0.8725 (m) cc_final: 0.8298 (p) REVERT: G 4259 SER cc_start: 0.8003 (p) cc_final: 0.7606 (m) REVERT: G 4379 ASN cc_start: 0.8778 (p0) cc_final: 0.8354 (p0) outliers start: 45 outliers final: 27 residues processed: 289 average time/residue: 0.1020 time to fit residues: 50.3605 Evaluate side-chains 225 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4364 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4364 VAL Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4239 THR Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4364 VAL Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4240 ILE Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4364 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4142 ASN C4084 ASN F4142 ASN G4084 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109965 restraints weight = 21649.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109719 restraints weight = 16989.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.110424 restraints weight = 15860.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111478 restraints weight = 11450.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.111556 restraints weight = 9376.141| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18137 Z= 0.222 Angle : 0.607 6.928 25151 Z= 0.323 Chirality : 0.048 0.194 3115 Planarity : 0.005 0.058 3255 Dihedral : 5.126 23.016 2527 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.32 % Allowed : 16.67 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2422 helix: None (None), residues: 0 sheet: -0.29 (0.17), residues: 903 loop : 0.55 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E4244 TYR 0.013 0.002 TYR F4139 PHE 0.018 0.002 PHE E4399 TRP 0.010 0.002 TRP G4191 HIS 0.003 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00545 (18109) covalent geometry : angle 0.60404 (25095) SS BOND : bond 0.00236 ( 28) SS BOND : angle 1.43634 ( 56) hydrogen bonds : bond 0.03899 ( 490) hydrogen bonds : angle 5.36178 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 195 time to evaluate : 0.751 Fit side-chains REVERT: B 4259 SER cc_start: 0.8257 (p) cc_final: 0.7772 (m) REVERT: A 4368 TYR cc_start: 0.9062 (m-80) cc_final: 0.8701 (m-80) REVERT: C 4154 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7580 (tt0) REVERT: C 4216 SER cc_start: 0.8599 (m) cc_final: 0.8142 (p) REVERT: C 4368 TYR cc_start: 0.9061 (m-80) cc_final: 0.8665 (m-80) REVERT: F 4117 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8358 (tm-30) REVERT: F 4259 SER cc_start: 0.8049 (p) cc_final: 0.7574 (m) REVERT: G 4216 SER cc_start: 0.8830 (m) cc_final: 0.8421 (p) REVERT: G 4259 SER cc_start: 0.8241 (p) cc_final: 0.7763 (m) outliers start: 68 outliers final: 54 residues processed: 249 average time/residue: 0.0962 time to fit residues: 40.8368 Evaluate side-chains 235 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4101 THR Chi-restraints excluded: chain B residue 4149 LEU Chi-restraints excluded: chain B residue 4153 VAL Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4269 ILE Chi-restraints excluded: chain B residue 4306 THR Chi-restraints excluded: chain B residue 4308 SER Chi-restraints excluded: chain B residue 4311 THR Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain B residue 4391 VAL Chi-restraints excluded: chain A residue 4082 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4085 VAL Chi-restraints excluded: chain C residue 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4239 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain C residue 4397 THR Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4101 THR Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4153 VAL Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4278 SER Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4082 THR Chi-restraints excluded: chain E residue 4101 THR Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain F residue 4339 VAL Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4120 LEU Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4371 THR Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 231 optimal weight: 0.0040 chunk 125 optimal weight: 0.0670 chunk 142 optimal weight: 0.9980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4302 ASN C4084 ASN F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117883 restraints weight = 21217.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118419 restraints weight = 15695.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118808 restraints weight = 13827.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119193 restraints weight = 11102.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120747 restraints weight = 9547.282| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18137 Z= 0.095 Angle : 0.511 6.840 25151 Z= 0.267 Chirality : 0.045 0.139 3115 Planarity : 0.005 0.048 3255 Dihedral : 4.475 20.133 2527 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.39 % Allowed : 17.60 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2422 helix: -3.83 (0.34), residues: 42 sheet: -0.26 (0.17), residues: 917 loop : 0.61 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B4075 TYR 0.012 0.001 TYR D4233 PHE 0.019 0.001 PHE E4399 TRP 0.013 0.001 TRP E4370 HIS 0.002 0.001 HIS D4137 Details of bonding type rmsd covalent geometry : bond 0.00227 (18109) covalent geometry : angle 0.50986 (25095) SS BOND : bond 0.00153 ( 28) SS BOND : angle 0.78167 ( 56) hydrogen bonds : bond 0.02887 ( 490) hydrogen bonds : angle 5.00913 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.467 Fit side-chains REVERT: B 4259 SER cc_start: 0.8106 (p) cc_final: 0.7611 (m) REVERT: B 4379 ASN cc_start: 0.8532 (p0) cc_final: 0.8285 (p0) REVERT: A 4368 TYR cc_start: 0.8971 (m-80) cc_final: 0.8510 (m-80) REVERT: C 4154 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7549 (tt0) REVERT: E 4379 ASN cc_start: 0.8830 (p0) cc_final: 0.8474 (p0) REVERT: F 4117 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 4163 ILE cc_start: 0.8973 (mm) cc_final: 0.8736 (mm) REVERT: F 4216 SER cc_start: 0.8755 (m) cc_final: 0.8223 (p) REVERT: F 4259 SER cc_start: 0.7876 (p) cc_final: 0.7415 (m) REVERT: G 4163 ILE cc_start: 0.9030 (mm) cc_final: 0.8603 (tt) REVERT: G 4216 SER cc_start: 0.8753 (m) cc_final: 0.8320 (p) REVERT: G 4259 SER cc_start: 0.8092 (p) cc_final: 0.7640 (m) REVERT: G 4379 ASN cc_start: 0.8850 (p0) cc_final: 0.8409 (p0) outliers start: 49 outliers final: 43 residues processed: 248 average time/residue: 0.1020 time to fit residues: 42.9175 Evaluate side-chains 236 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4149 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4269 ILE Chi-restraints excluded: chain B residue 4311 THR Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain B residue 4391 VAL Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4364 VAL Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4085 VAL Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4364 VAL Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4082 THR Chi-restraints excluded: chain D residue 4101 THR Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4364 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4120 LEU Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Chi-restraints excluded: chain G residue 4400 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 221 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 197 optimal weight: 0.0870 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4142 ASN F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116427 restraints weight = 21304.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116624 restraints weight = 16171.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117377 restraints weight = 14440.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117922 restraints weight = 10945.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.118116 restraints weight = 9410.812| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18137 Z= 0.127 Angle : 0.527 6.855 25151 Z= 0.275 Chirality : 0.045 0.145 3115 Planarity : 0.005 0.051 3255 Dihedral : 4.530 20.254 2527 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.39 % Allowed : 18.14 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2422 helix: -3.79 (0.35), residues: 42 sheet: -0.21 (0.17), residues: 917 loop : 0.62 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B4075 TYR 0.011 0.001 TYR F4139 PHE 0.017 0.001 PHE E4399 TRP 0.011 0.001 TRP E4370 HIS 0.002 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00311 (18109) covalent geometry : angle 0.52556 (25095) SS BOND : bond 0.00102 ( 28) SS BOND : angle 0.88452 ( 56) hydrogen bonds : bond 0.03135 ( 490) hydrogen bonds : angle 4.99685 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.681 Fit side-chains REVERT: B 4259 SER cc_start: 0.8169 (p) cc_final: 0.7666 (m) REVERT: B 4379 ASN cc_start: 0.8573 (p0) cc_final: 0.8340 (p0) REVERT: A 4368 TYR cc_start: 0.9002 (m-80) cc_final: 0.8545 (m-80) REVERT: A 4379 ASN cc_start: 0.8835 (p0) cc_final: 0.8329 (p0) REVERT: C 4154 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7540 (tt0) REVERT: C 4216 SER cc_start: 0.8532 (m) cc_final: 0.8098 (p) REVERT: D 4379 ASN cc_start: 0.8803 (p0) cc_final: 0.8303 (p0) REVERT: E 4379 ASN cc_start: 0.8848 (p0) cc_final: 0.8498 (p0) REVERT: F 4117 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 4163 ILE cc_start: 0.9009 (mm) cc_final: 0.8771 (mm) REVERT: F 4259 SER cc_start: 0.7948 (p) cc_final: 0.7484 (m) REVERT: G 4163 ILE cc_start: 0.9059 (mm) cc_final: 0.8810 (mm) REVERT: G 4216 SER cc_start: 0.8766 (m) cc_final: 0.8362 (p) REVERT: G 4259 SER cc_start: 0.8135 (p) cc_final: 0.7638 (m) REVERT: G 4379 ASN cc_start: 0.8869 (p0) cc_final: 0.8429 (p0) outliers start: 49 outliers final: 42 residues processed: 242 average time/residue: 0.1032 time to fit residues: 42.5725 Evaluate side-chains 234 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4149 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4269 ILE Chi-restraints excluded: chain B residue 4311 THR Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4387 SER Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4085 VAL Chi-restraints excluded: chain C residue 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4101 THR Chi-restraints excluded: chain D residue 4120 LEU Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4082 THR Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain F residue 4339 VAL Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4101 THR Chi-restraints excluded: chain G residue 4107 SER Chi-restraints excluded: chain G residue 4120 LEU Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4084 ASN ** G4142 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 = 0.3409 r_free = 0.3409 target = 0.131887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117416 restraints weight = 21210.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117433 restraints weight = 16108.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.117809 restraints weight = 16919.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118935 restraints weight = 12070.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119049 restraints weight = 9502.623| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18137 Z= 0.116 Angle : 0.519 6.856 25151 Z= 0.270 Chirality : 0.045 0.160 3115 Planarity : 0.005 0.049 3255 Dihedral : 4.455 21.476 2527 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.39 % Allowed : 18.14 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2422 helix: -3.77 (0.35), residues: 42 sheet: -0.16 (0.17), residues: 917 loop : 0.63 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B4075 TYR 0.012 0.001 TYR F4139 PHE 0.017 0.001 PHE D4399 TRP 0.011 0.001 TRP E4370 HIS 0.002 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00283 (18109) covalent geometry : angle 0.51775 (25095) SS BOND : bond 0.00103 ( 28) SS BOND : angle 0.80275 ( 56) hydrogen bonds : bond 0.03029 ( 490) hydrogen bonds : angle 4.92754 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.740 Fit side-chains REVERT: B 4259 SER cc_start: 0.8175 (p) cc_final: 0.7664 (m) REVERT: A 4368 TYR cc_start: 0.8988 (m-80) cc_final: 0.8525 (m-80) REVERT: A 4379 ASN cc_start: 0.8822 (p0) cc_final: 0.8318 (p0) REVERT: C 4154 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7516 (tt0) REVERT: C 4216 SER cc_start: 0.8517 (m) cc_final: 0.8080 (p) REVERT: C 4364 VAL cc_start: 0.8853 (m) cc_final: 0.8575 (m) REVERT: D 4379 ASN cc_start: 0.8788 (p0) cc_final: 0.8329 (p0) REVERT: E 4379 ASN cc_start: 0.8840 (p0) cc_final: 0.8502 (p0) REVERT: F 4117 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8308 (tm-30) REVERT: F 4163 ILE cc_start: 0.8937 (mm) cc_final: 0.8684 (mm) REVERT: F 4259 SER cc_start: 0.7885 (p) cc_final: 0.7437 (m) REVERT: G 4163 ILE cc_start: 0.9039 (mm) cc_final: 0.8787 (mm) REVERT: G 4216 SER cc_start: 0.8761 (m) cc_final: 0.8359 (p) REVERT: G 4259 SER cc_start: 0.8072 (p) cc_final: 0.7545 (m) REVERT: G 4379 ASN cc_start: 0.8861 (p0) cc_final: 0.8416 (p0) outliers start: 49 outliers final: 44 residues processed: 239 average time/residue: 0.1098 time to fit residues: 44.6838 Evaluate side-chains 238 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4107 SER Chi-restraints excluded: chain B residue 4149 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4269 ILE Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4355 ASP Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4082 THR Chi-restraints excluded: chain C residue 4085 VAL Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain C residue 4391 VAL Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4082 THR Chi-restraints excluded: chain D residue 4101 THR Chi-restraints excluded: chain D residue 4120 LEU Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain D residue 4391 VAL Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4257 ILE Chi-restraints excluded: chain E residue 4286 THR Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4240 ILE Chi-restraints excluded: chain F residue 4286 THR Chi-restraints excluded: chain F residue 4339 VAL Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4101 THR Chi-restraints excluded: chain G residue 4107 SER Chi-restraints excluded: chain G residue 4120 LEU Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4395 THR Chi-restraints excluded: chain G residue 4400 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 86 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.111870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096001 restraints weight = 22437.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.095890 restraints weight = 20132.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096213 restraints weight = 18588.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.096855 restraints weight = 15148.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.096999 restraints weight = 13303.166| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18137 Z= 0.176 Angle : 0.563 6.918 25151 Z= 0.296 Chirality : 0.047 0.174 3115 Planarity : 0.005 0.055 3255 Dihedral : 4.771 21.360 2527 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 17.99 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2422 helix: None (None), residues: 0 sheet: -0.07 (0.17), residues: 889 loop : 0.58 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A4244 TYR 0.013 0.001 TYR F4139 PHE 0.017 0.001 PHE D4399 TRP 0.009 0.001 TRP A4191 HIS 0.003 0.001 HIS B4137 Details of bonding type rmsd covalent geometry : bond 0.00432 (18109) covalent geometry : angle 0.56131 (25095) SS BOND : bond 0.00147 ( 28) SS BOND : angle 1.14462 ( 56) hydrogen bonds : bond 0.03492 ( 490) hydrogen bonds : angle 5.10013 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.43 seconds wall clock time: 45 minutes 48.82 seconds (2748.82 seconds total)