Starting phenix.real_space_refine on Tue Nov 19 01:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_50542.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_50542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_50542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_50542.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flx_50542/11_2024/9flx_50542.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17675 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F Time building chain proxies: 6.31, per 1000 atoms: 0.36 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=4, 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 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: 4.55 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 4.02 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: 7.64 Time building geometry restraints manager: 5.24 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: 9950 13.63 - 27.26: 445 27.26 - 40.89: 51 40.89 - 54.52: 30 54.52 - 68.15: 22 Dihedral angle restraints: 10498 sinusoidal: 3519 harmonic: 6979 Sorted by residual: dihedral pdb=" CB CYS B4186 " pdb=" SG CYS B4186 " pdb=" SG CYS B4236 " pdb=" CB CYS B4236 " ideal model delta sinusoidal sigma weight residual 93.00 37.17 55.83 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS B4092 " pdb=" SG CYS B4092 " pdb=" SG CYS B4243 " pdb=" CB CYS B4243 " ideal model delta sinusoidal sigma weight residual 93.00 136.74 -43.74 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" C PHE D4089 " pdb=" N PHE D4089 " pdb=" CA PHE D4089 " pdb=" CB PHE D4089 " ideal model delta harmonic sigma weight residual -122.60 -109.81 -12.79 0 2.50e+00 1.60e-01 2.62e+01 ... (remaining 10495 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: 2.03 - 2.60: 248 2.60 - 3.18: 15714 3.18 - 3.75: 27019 3.75 - 4.33: 37417 4.33 - 4.90: 59623 Nonbonded interactions: 140021 Sorted by model distance: nonbonded pdb=" SG CYS E4092 " pdb=" SG CYS E4243 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F4092 " pdb=" SG CYS F4243 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS A4092 " pdb=" SG CYS A4243 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C4092 " pdb=" SG CYS C4243 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D4092 " pdb=" SG CYS D4243 " model vdw 2.031 3.760 ... (remaining 140016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 39.910 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.670 ------------------------------------------------------------------------------- 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 18109 Z= 1.156 Angle : 1.518 11.783 25095 Z= 1.003 Chirality : 0.078 0.318 3115 Planarity : 0.008 0.028 3255 Dihedral : 9.300 68.146 6020 Min Nonbonded Distance : 2.030 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (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 TRP 0.030 0.005 TRP C4370 HIS 0.009 0.003 HIS C4137 PHE 0.051 0.007 PHE F4399 TYR 0.046 0.008 TYR A4233 ARG 0.001 0.000 ARG F4075 *********************** 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 : 1.863 Fit side-chains revert: symmetry clash REVERT: B 4154 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7818 (tt0) REVERT: B 4165 THR cc_start: 0.8203 (m) cc_final: 0.7968 (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: 0.6871 (m) REVERT: B 4278 SER cc_start: 0.8060 (p) cc_final: 0.7828 (t) REVERT: B 4308 SER cc_start: 0.8145 (p) cc_final: 0.7919 (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: 0.7782 (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: 0.7630 (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: 0.7270 (t0) REVERT: D 4368 TYR cc_start: 0.7756 (m-80) cc_final: 0.7431 (m-80) REVERT: D 4379 ASN cc_start: 0.7796 (p0) cc_final: 0.7578 (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: 0.6813 (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: 0.6782 (m-40) REVERT: F 4379 ASN cc_start: 0.7547 (p0) cc_final: 0.7163 (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: 0.7992 (t) REVERT: G 4216 SER cc_start: 0.8566 (m) cc_final: 0.7998 (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: 0.2064 time to fit residues: 183.4354 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 : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 E4185 ASN E4414 GLN F4147 GLN F4414 GLN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18109 Z= 0.219 Angle : 0.588 6.907 25095 Z= 0.324 Chirality : 0.047 0.151 3115 Planarity : 0.005 0.052 3255 Dihedral : 5.268 19.112 2527 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.17 % Allowed : 10.48 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2422 helix: -2.91 (0.61), residues: 42 sheet: 0.21 (0.16), residues: 875 loop : 0.70 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C4370 HIS 0.003 0.001 HIS D4137 PHE 0.017 0.002 PHE G4399 TYR 0.019 0.001 TYR D4233 ARG 0.001 0.000 ARG G4075 *********************** 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: 65 poor density : 317 time to evaluate : 1.893 Fit side-chains REVERT: B 4165 THR cc_start: 0.8295 (m) cc_final: 0.7799 (p) REVERT: B 4402 ASP cc_start: 0.7583 (t0) cc_final: 0.7193 (m-30) REVERT: A 4139 TYR cc_start: 0.8869 (p90) cc_final: 0.8586 (p90) REVERT: A 4379 ASN cc_start: 0.7883 (p0) cc_final: 0.7601 (p0) REVERT: A 4402 ASP cc_start: 0.7822 (t0) cc_final: 0.7466 (m-30) REVERT: C 4302 ASN cc_start: 0.7504 (m-40) cc_final: 0.7216 (t0) REVERT: D 4139 TYR cc_start: 0.8908 (p90) cc_final: 0.8582 (p90) REVERT: D 4176 ASP cc_start: 0.7678 (m-30) cc_final: 0.7191 (m-30) REVERT: D 4302 ASN cc_start: 0.7484 (m-40) cc_final: 0.7217 (t0) REVERT: D 4379 ASN cc_start: 0.8090 (p0) cc_final: 0.7855 (p0) REVERT: E 4302 ASN cc_start: 0.7467 (m-40) cc_final: 0.7030 (t0) REVERT: E 4379 ASN cc_start: 0.7883 (p0) cc_final: 0.7581 (p0) REVERT: F 4165 THR cc_start: 0.7929 (m) cc_final: 0.7596 (p) REVERT: F 4302 ASN cc_start: 0.7184 (m-40) cc_final: 0.6901 (t0) REVERT: F 4402 ASP cc_start: 0.7564 (t0) cc_final: 0.6961 (m-30) REVERT: G 4165 THR cc_start: 0.8195 (m) cc_final: 0.7663 (t) REVERT: G 4216 SER cc_start: 0.8309 (m) cc_final: 0.7917 (p) REVERT: G 4238 ASP cc_start: 0.7820 (t0) cc_final: 0.7373 (t0) REVERT: G 4259 SER cc_start: 0.7406 (p) cc_final: 0.7172 (m) REVERT: G 4379 ASN cc_start: 0.7926 (p0) cc_final: 0.7685 (p0) outliers start: 65 outliers final: 42 residues processed: 355 average time/residue: 0.2187 time to fit residues: 131.8931 Evaluate side-chains 254 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4075 ARG Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4397 THR Chi-restraints excluded: chain A residue 4075 ARG Chi-restraints excluded: chain A residue 4099 LEU Chi-restraints excluded: chain A residue 4107 SER 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 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 4259 SER Chi-restraints excluded: chain C residue 4397 THR Chi-restraints excluded: chain D residue 4099 LEU 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 4308 SER 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 4286 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 4107 SER 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 4308 SER Chi-restraints excluded: chain G residue 4106 THR Chi-restraints excluded: chain G residue 4167 THR Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4387 SER 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 120 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4142 ASN ** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4142 ASN E4142 ASN E4185 ASN F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18109 Z= 0.438 Angle : 0.659 6.316 25095 Z= 0.356 Chirality : 0.050 0.152 3115 Planarity : 0.006 0.053 3255 Dihedral : 5.450 18.502 2527 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.63 % Allowed : 12.29 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2422 helix: -3.43 (0.46), residues: 42 sheet: -0.17 (0.16), residues: 938 loop : 0.60 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F4232 HIS 0.005 0.002 HIS D4137 PHE 0.014 0.002 PHE C4399 TYR 0.018 0.002 TYR F4139 ARG 0.002 0.000 ARG D4075 *********************** 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 325 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 230 time to evaluate : 1.775 Fit side-chains REVERT: A 4368 TYR cc_start: 0.8512 (m-80) cc_final: 0.8175 (m-80) REVERT: A 4379 ASN cc_start: 0.8313 (p0) cc_final: 0.8104 (p0) REVERT: A 4402 ASP cc_start: 0.7978 (t0) cc_final: 0.7679 (t0) REVERT: D 4176 ASP cc_start: 0.7651 (m-30) cc_final: 0.7278 (m-30) REVERT: D 4287 TYR cc_start: 0.7626 (m-80) cc_final: 0.7320 (m-80) REVERT: E 4246 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7454 (tt0) REVERT: F 4238 ASP cc_start: 0.8152 (t0) cc_final: 0.7827 (t0) REVERT: F 4302 ASN cc_start: 0.7329 (m-40) cc_final: 0.7126 (m-40) REVERT: G 4104 ASN cc_start: 0.7728 (m-40) cc_final: 0.7525 (m-40) REVERT: G 4216 SER cc_start: 0.8440 (m) cc_final: 0.7815 (p) REVERT: G 4238 ASP cc_start: 0.8118 (t0) cc_final: 0.7856 (t0) REVERT: G 4269 ILE cc_start: 0.6578 (mm) cc_final: 0.6207 (pt) REVERT: G 4379 ASN cc_start: 0.8290 (p0) cc_final: 0.8058 (p0) outliers start: 95 outliers final: 74 residues processed: 297 average time/residue: 0.2263 time to fit residues: 113.4356 Evaluate side-chains 268 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 194 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 4179 THR Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4259 SER 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 4339 VAL 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 4306 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4339 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 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 4387 SER Chi-restraints excluded: chain C residue 4397 THR 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 4173 CYS Chi-restraints excluded: chain D residue 4179 THR Chi-restraints excluded: chain D residue 4260 THR Chi-restraints excluded: chain D residue 4306 THR 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 4075 ARG Chi-restraints excluded: chain E residue 4107 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 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 F residue 4099 LEU Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4118 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS 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 4339 VAL Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain G residue 4075 ARG Chi-restraints excluded: chain G residue 4101 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 4286 THR 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 213 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18109 Z= 0.237 Angle : 0.552 6.726 25095 Z= 0.294 Chirality : 0.046 0.148 3115 Planarity : 0.005 0.053 3255 Dihedral : 4.973 21.617 2527 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.46 % Allowed : 14.48 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2422 helix: -3.68 (0.38), residues: 42 sheet: -0.07 (0.17), residues: 875 loop : 0.60 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C4370 HIS 0.003 0.001 HIS A4137 PHE 0.019 0.001 PHE G4399 TYR 0.017 0.001 TYR A4139 ARG 0.001 0.000 ARG E4244 *********************** 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 300 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 2.228 Fit side-chains REVERT: A 4368 TYR cc_start: 0.8513 (m-80) cc_final: 0.8057 (m-80) REVERT: A 4379 ASN cc_start: 0.8379 (p0) cc_final: 0.8177 (p0) REVERT: A 4402 ASP cc_start: 0.7921 (t0) cc_final: 0.7630 (t0) REVERT: D 4104 ASN cc_start: 0.7828 (m-40) cc_final: 0.7572 (m-40) REVERT: D 4176 ASP cc_start: 0.7706 (m-30) cc_final: 0.7202 (m-30) REVERT: E 4238 ASP cc_start: 0.8103 (t0) cc_final: 0.7851 (t0) REVERT: E 4269 ILE cc_start: 0.6654 (mm) cc_final: 0.6304 (pt) REVERT: G 4238 ASP cc_start: 0.8125 (t0) cc_final: 0.7855 (t0) REVERT: G 4269 ILE cc_start: 0.6617 (mm) cc_final: 0.6347 (pt) outliers start: 71 outliers final: 52 residues processed: 283 average time/residue: 0.2203 time to fit residues: 105.3722 Evaluate side-chains 240 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 A residue 4167 THR Chi-restraints excluded: chain A residue 4222 SER Chi-restraints excluded: chain A residue 4270 CYS Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER 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 4234 MET Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4308 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 4257 ILE Chi-restraints excluded: chain D residue 4270 CYS Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4075 ARG 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 4286 THR Chi-restraints excluded: chain E residue 4308 SER Chi-restraints excluded: chain F residue 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS 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 4308 SER Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain G residue 4107 SER Chi-restraints excluded: chain G residue 4210 VAL Chi-restraints excluded: chain G residue 4257 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 Chi-restraints excluded: chain G residue 4397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4185 ASN D4302 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18109 Z= 0.331 Angle : 0.585 6.921 25095 Z= 0.312 Chirality : 0.047 0.151 3115 Planarity : 0.005 0.056 3255 Dihedral : 5.063 17.673 2527 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.83 % Allowed : 15.07 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2422 helix: -3.96 (0.30), residues: 42 sheet: -0.25 (0.17), residues: 875 loop : 0.52 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E4191 HIS 0.003 0.001 HIS G4137 PHE 0.018 0.002 PHE G4399 TYR 0.013 0.001 TYR F4139 ARG 0.001 0.000 ARG A4244 *********************** 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 302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 203 time to evaluate : 1.961 Fit side-chains REVERT: A 4368 TYR cc_start: 0.8562 (m-80) cc_final: 0.8261 (m-80) REVERT: A 4402 ASP cc_start: 0.7935 (t0) cc_final: 0.7604 (t0) REVERT: C 4246 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7504 (tt0) REVERT: C 4368 TYR cc_start: 0.8520 (m-80) cc_final: 0.8177 (m-80) REVERT: D 4176 ASP cc_start: 0.7694 (m-30) cc_final: 0.7283 (m-30) REVERT: D 4379 ASN cc_start: 0.8648 (p0) cc_final: 0.8308 (p0) REVERT: D 4402 ASP cc_start: 0.7996 (t0) cc_final: 0.7646 (t0) REVERT: D 4406 CYS cc_start: 0.8861 (m) cc_final: 0.8618 (p) outliers start: 99 outliers final: 74 residues processed: 281 average time/residue: 0.2383 time to fit residues: 113.7337 Evaluate side-chains 255 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 4259 SER Chi-restraints excluded: chain B residue 4260 THR Chi-restraints excluded: chain B residue 4302 ASN 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 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 4222 SER Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4339 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 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4179 THR Chi-restraints excluded: chain C residue 4234 MET Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4308 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 4173 CYS Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4306 THR Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4075 ARG Chi-restraints excluded: chain E residue 4100 THR 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 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 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS Chi-restraints excluded: chain F residue 4179 THR 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 4339 VAL Chi-restraints excluded: chain F residue 4387 SER 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 4210 VAL Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4306 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 77 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C4185 ASN E4142 ASN F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18109 Z= 0.329 Angle : 0.583 6.974 25095 Z= 0.310 Chirality : 0.047 0.145 3115 Planarity : 0.005 0.058 3255 Dihedral : 5.040 17.165 2527 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.78 % Allowed : 15.11 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2422 helix: -4.19 (0.24), residues: 42 sheet: -0.35 (0.16), residues: 875 loop : 0.41 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4370 HIS 0.003 0.001 HIS B4137 PHE 0.019 0.002 PHE G4399 TYR 0.012 0.001 TYR D4233 ARG 0.000 0.000 ARG A4244 *********************** 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 283 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 185 time to evaluate : 1.636 Fit side-chains REVERT: A 4368 TYR cc_start: 0.8604 (m-80) cc_final: 0.8363 (m-80) REVERT: A 4402 ASP cc_start: 0.8004 (t0) cc_final: 0.7691 (t0) REVERT: C 4368 TYR cc_start: 0.8520 (m-80) cc_final: 0.8206 (m-80) REVERT: D 4176 ASP cc_start: 0.7702 (m-30) cc_final: 0.7320 (m-30) REVERT: D 4379 ASN cc_start: 0.8685 (p0) cc_final: 0.8328 (p0) REVERT: D 4402 ASP cc_start: 0.8001 (t0) cc_final: 0.7649 (t0) REVERT: D 4406 CYS cc_start: 0.8923 (m) cc_final: 0.8649 (p) REVERT: G 4216 SER cc_start: 0.8413 (m) cc_final: 0.7679 (p) outliers start: 98 outliers final: 84 residues processed: 258 average time/residue: 0.2296 time to fit residues: 101.6819 Evaluate side-chains 254 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 170 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 4167 THR Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4259 SER Chi-restraints excluded: chain B residue 4260 THR 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 4100 THR Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4222 SER Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4339 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 4107 SER Chi-restraints excluded: chain C residue 4167 THR Chi-restraints excluded: chain C residue 4185 ASN Chi-restraints excluded: chain C residue 4234 MET Chi-restraints excluded: chain C residue 4257 ILE Chi-restraints excluded: chain C residue 4259 SER Chi-restraints excluded: chain C residue 4308 SER Chi-restraints excluded: chain C residue 4339 VAL Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain D residue 4075 ARG Chi-restraints excluded: chain D residue 4100 THR 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 4153 VAL Chi-restraints excluded: chain D residue 4173 CYS Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4260 THR Chi-restraints excluded: chain D residue 4269 ILE Chi-restraints excluded: chain D residue 4306 THR Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4075 ARG 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 4210 VAL 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 4306 THR Chi-restraints excluded: chain E residue 4308 SER 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 4107 SER Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS 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 4339 VAL Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain F residue 4406 CYS 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 4153 VAL Chi-restraints excluded: chain G residue 4210 VAL Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4306 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 Chi-restraints excluded: chain G residue 4397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 193 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 C4185 ASN ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4142 ASN ** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18109 Z= 0.305 Angle : 0.573 7.006 25095 Z= 0.303 Chirality : 0.047 0.162 3115 Planarity : 0.005 0.052 3255 Dihedral : 4.974 16.871 2527 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.07 % Allowed : 15.36 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2422 helix: None (None), residues: 0 sheet: -0.37 (0.16), residues: 875 loop : 0.40 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4370 HIS 0.003 0.001 HIS G4137 PHE 0.019 0.002 PHE G4399 TYR 0.017 0.001 TYR F4139 ARG 0.001 0.000 ARG A4244 *********************** 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 289 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 185 time to evaluate : 1.921 Fit side-chains REVERT: A 4402 ASP cc_start: 0.8019 (t0) cc_final: 0.7707 (t0) REVERT: C 4368 TYR cc_start: 0.8516 (m-80) cc_final: 0.8206 (m-80) REVERT: D 4176 ASP cc_start: 0.7710 (m-30) cc_final: 0.7325 (m-30) REVERT: D 4379 ASN cc_start: 0.8704 (p0) cc_final: 0.8338 (p0) REVERT: D 4402 ASP cc_start: 0.7981 (t0) cc_final: 0.7636 (t0) REVERT: D 4406 CYS cc_start: 0.8942 (m) cc_final: 0.8662 (p) REVERT: G 4216 SER cc_start: 0.8402 (m) cc_final: 0.7702 (p) outliers start: 104 outliers final: 94 residues processed: 259 average time/residue: 0.2514 time to fit residues: 110.0429 Evaluate side-chains 264 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 170 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 4210 VAL Chi-restraints excluded: chain B residue 4239 THR Chi-restraints excluded: chain B residue 4240 ILE Chi-restraints excluded: chain B residue 4257 ILE Chi-restraints excluded: chain B residue 4259 SER Chi-restraints excluded: chain B residue 4260 THR Chi-restraints excluded: chain B residue 4271 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 4377 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 4100 THR Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4153 VAL Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4222 SER Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER Chi-restraints excluded: chain A residue 4339 VAL 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 4107 SER Chi-restraints excluded: chain C residue 4153 VAL 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 4283 SER Chi-restraints excluded: chain C residue 4308 SER Chi-restraints excluded: chain C residue 4339 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 4100 THR 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 4173 CYS Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4260 THR Chi-restraints excluded: chain D residue 4306 THR Chi-restraints excluded: chain D residue 4339 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4100 THR Chi-restraints excluded: chain E residue 4101 THR Chi-restraints excluded: chain E residue 4107 SER Chi-restraints excluded: chain E residue 4153 VAL 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 4286 THR Chi-restraints excluded: chain E residue 4306 THR Chi-restraints excluded: chain E residue 4308 SER Chi-restraints excluded: chain E residue 4311 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 4107 SER Chi-restraints excluded: chain F residue 4153 VAL Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS 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 4283 SER 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 4339 VAL Chi-restraints excluded: chain F residue 4387 SER Chi-restraints excluded: chain F residue 4406 CYS 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 4210 VAL Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4306 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 Chi-restraints excluded: chain G residue 4397 THR Chi-restraints excluded: chain G residue 4406 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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** D4142 ASN G4185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18109 Z= 0.212 Angle : 0.532 6.891 25095 Z= 0.280 Chirality : 0.045 0.144 3115 Planarity : 0.005 0.049 3255 Dihedral : 4.672 15.295 2527 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.39 % Allowed : 16.04 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2422 helix: -4.32 (0.22), residues: 42 sheet: -0.24 (0.17), residues: 875 loop : 0.42 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4370 HIS 0.002 0.001 HIS B4137 PHE 0.019 0.001 PHE G4399 TYR 0.013 0.001 TYR F4139 ARG 0.000 0.000 ARG F4075 *********************** 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 296 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 206 time to evaluate : 2.001 Fit side-chains REVERT: A 4402 ASP cc_start: 0.8001 (t0) cc_final: 0.7689 (t0) REVERT: D 4176 ASP cc_start: 0.7742 (m-30) cc_final: 0.7323 (m-30) REVERT: D 4379 ASN cc_start: 0.8700 (p0) cc_final: 0.8332 (p0) REVERT: D 4402 ASP cc_start: 0.7963 (t0) cc_final: 0.7624 (t0) REVERT: E 4269 ILE cc_start: 0.6907 (mm) cc_final: 0.6516 (pt) outliers start: 90 outliers final: 78 residues processed: 275 average time/residue: 0.2234 time to fit residues: 103.8322 Evaluate side-chains 254 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4082 THR 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 4257 ILE Chi-restraints excluded: chain B residue 4259 SER Chi-restraints excluded: chain B residue 4260 THR Chi-restraints excluded: chain B residue 4269 ILE Chi-restraints excluded: chain B residue 4271 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 4377 THR Chi-restraints excluded: chain B residue 4387 SER Chi-restraints excluded: chain B residue 4391 VAL Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4153 VAL Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4222 SER Chi-restraints excluded: chain A residue 4259 SER Chi-restraints excluded: chain A residue 4270 CYS Chi-restraints excluded: chain A residue 4283 SER Chi-restraints excluded: chain A residue 4306 THR Chi-restraints excluded: chain A residue 4308 SER 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 4153 VAL 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 4283 SER Chi-restraints excluded: chain C residue 4387 SER Chi-restraints excluded: chain C residue 4406 CYS 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 4153 VAL Chi-restraints excluded: chain D residue 4173 CYS Chi-restraints excluded: chain D residue 4257 ILE Chi-restraints excluded: chain D residue 4259 SER Chi-restraints excluded: chain D residue 4260 THR 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 4210 VAL 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 4306 THR Chi-restraints excluded: chain E residue 4364 VAL Chi-restraints excluded: chain E residue 4400 ILE Chi-restraints excluded: chain F residue 4153 VAL Chi-restraints excluded: chain F residue 4167 THR Chi-restraints excluded: chain F residue 4173 CYS Chi-restraints excluded: chain F residue 4240 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 4387 SER Chi-restraints excluded: chain F residue 4406 CYS 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 4153 VAL Chi-restraints excluded: chain G residue 4210 VAL Chi-restraints excluded: chain G residue 4240 ILE Chi-restraints excluded: chain G residue 4286 THR Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4380 LEU Chi-restraints excluded: chain G residue 4387 SER Chi-restraints excluded: chain G residue 4395 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 1.9990 chunk 219 optimal weight: 0.0870 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 128 optimal weight: 0.0030 chunk 93 optimal weight: 0.0770 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 193 optimal weight: 0.0050 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.2340 ------------------------------------------------------------------------------- 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 A4142 ASN C4084 ASN ** F4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18109 Z= 0.135 Angle : 0.490 7.182 25095 Z= 0.255 Chirality : 0.044 0.155 3115 Planarity : 0.004 0.041 3255 Dihedral : 4.200 22.056 2527 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.19 % Allowed : 18.72 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2422 helix: -4.23 (0.26), residues: 42 sheet: -0.12 (0.17), residues: 910 loop : 0.55 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E4370 HIS 0.002 0.001 HIS B4137 PHE 0.020 0.001 PHE E4399 TYR 0.012 0.001 TYR D4233 ARG 0.001 0.000 ARG A4075 *********************** 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 285 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 2.039 Fit side-chains REVERT: B 4302 ASN cc_start: 0.7229 (m-40) cc_final: 0.6995 (m110) REVERT: B 4402 ASP cc_start: 0.8140 (t0) cc_final: 0.7765 (t0) REVERT: A 4379 ASN cc_start: 0.8382 (p0) cc_final: 0.8178 (p0) REVERT: A 4402 ASP cc_start: 0.7995 (t0) cc_final: 0.7650 (t0) REVERT: C 4302 ASN cc_start: 0.6842 (m-40) cc_final: 0.6312 (t0) REVERT: D 4176 ASP cc_start: 0.7679 (m-30) cc_final: 0.7212 (m-30) REVERT: D 4402 ASP cc_start: 0.7820 (t0) cc_final: 0.7529 (t0) REVERT: E 4269 ILE cc_start: 0.6967 (mm) cc_final: 0.6611 (pt) REVERT: F 4302 ASN cc_start: 0.7180 (m110) cc_final: 0.6867 (m110) outliers start: 45 outliers final: 32 residues processed: 271 average time/residue: 0.2185 time to fit residues: 100.4667 Evaluate side-chains 230 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4082 THR 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 4257 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 A residue 4082 THR Chi-restraints excluded: chain A residue 4107 SER Chi-restraints excluded: chain A residue 4364 VAL Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4153 VAL Chi-restraints excluded: chain C residue 4283 SER Chi-restraints excluded: chain C residue 4339 VAL 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 4101 THR Chi-restraints excluded: chain D residue 4130 LEU Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain E residue 4100 THR Chi-restraints excluded: chain E residue 4101 THR Chi-restraints excluded: chain E residue 4167 THR Chi-restraints excluded: chain E residue 4240 ILE 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 4101 THR 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 226 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4142 ASN ** F4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4084 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18109 Z= 0.311 Angle : 0.571 7.066 25095 Z= 0.300 Chirality : 0.047 0.141 3115 Planarity : 0.005 0.053 3255 Dihedral : 4.698 21.579 2527 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 20.09 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2422 helix: None (None), residues: 0 sheet: -0.00 (0.17), residues: 875 loop : 0.46 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D4370 HIS 0.003 0.001 HIS A4137 PHE 0.019 0.002 PHE G4399 TYR 0.014 0.001 TYR F4139 ARG 0.001 0.000 ARG C4244 ********************** 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 233 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 1.953 Fit side-chains REVERT: A 4402 ASP cc_start: 0.8018 (t0) cc_final: 0.7704 (t0) REVERT: D 4176 ASP cc_start: 0.7723 (m-30) cc_final: 0.7326 (m-30) REVERT: D 4402 ASP cc_start: 0.7934 (t0) cc_final: 0.7646 (t0) REVERT: E 4269 ILE cc_start: 0.6979 (mm) cc_final: 0.6582 (pt) outliers start: 39 outliers final: 34 residues processed: 223 average time/residue: 0.2260 time to fit residues: 84.5604 Evaluate side-chains 221 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4082 THR 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 4257 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 A residue 4082 THR Chi-restraints excluded: chain A residue 4400 ILE Chi-restraints excluded: chain C residue 4153 VAL Chi-restraints excluded: chain C residue 4283 SER Chi-restraints excluded: chain C residue 4339 VAL 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 4130 LEU Chi-restraints excluded: chain D residue 4153 VAL Chi-restraints excluded: chain D residue 4387 SER Chi-restraints excluded: chain D residue 4391 VAL 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 4400 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 4306 THR Chi-restraints excluded: chain G residue 4100 THR Chi-restraints excluded: chain G residue 4101 THR Chi-restraints excluded: chain G residue 4153 VAL Chi-restraints excluded: chain G residue 4257 ILE Chi-restraints excluded: chain G residue 4380 LEU 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 201 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F4142 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 = 0.3094 r_free = 0.3094 target = 0.109021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.091768 restraints weight = 23452.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.093391 restraints weight = 15733.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094469 restraints weight = 11694.585| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18109 Z= 0.163 Angle : 0.509 6.924 25095 Z= 0.265 Chirality : 0.045 0.141 3115 Planarity : 0.005 0.048 3255 Dihedral : 4.330 19.461 2527 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.51 % Allowed : 20.53 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2422 helix: -4.28 (0.25), residues: 42 sheet: -0.05 (0.17), residues: 903 loop : 0.55 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E4370 HIS 0.002 0.001 HIS A4137 PHE 0.019 0.001 PHE G4399 TYR 0.013 0.001 TYR F4139 ARG 0.000 0.000 ARG A4075 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.87 seconds wall clock time: 60 minutes 43.55 seconds (3643.55 seconds total)