Starting phenix.real_space_refine on Tue Feb 3 20:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.map" model { file = "/net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pgo_71636/02_2026/9pgo_71636.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 12 5.16 5 C 4248 2.51 5 N 1224 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6756 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "G" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "H" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "J" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "K" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "L" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 1.22, per 1000 atoms: 0.18 Number of scatterers: 6756 At special positions: 0 Unit cell: (107.586, 130.938, 50.04, 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 12 16.00 O 1272 8.00 N 1224 7.00 C 4248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.53 Conformation dependent library (CDL) restraints added in 257.9 milliseconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.404A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL D 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.281A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.256A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 356 removed outlier: 8.444A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE B 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.477A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN C 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS D 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 365 through 366 removed outlier: 4.210A pdb=" N GLY A 365 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 365 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C 365 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D 365 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY E 365 " --> pdb=" O GLY F 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 369 through 377 Processing sheet with id=AB4, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.409A pdb=" N VAL G 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL H 309 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE G 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL H 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL I 309 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE H 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL I 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL J 309 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE I 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL J 306 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL K 309 " --> pdb=" O VAL J 306 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE J 308 " --> pdb=" O VAL K 309 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL K 306 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL L 309 " --> pdb=" O VAL K 306 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE K 308 " --> pdb=" O VAL L 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 313 through 314 Processing sheet with id=AB6, first strand: chain 'G' and resid 317 through 318 Processing sheet with id=AB7, first strand: chain 'G' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.285A pdb=" N ILE G 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE H 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE I 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE J 328 " --> pdb=" O HIS K 329 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE K 328 " --> pdb=" O HIS L 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 336 through 340 Processing sheet with id=AC1, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AC2, first strand: chain 'G' and resid 350 through 351 removed outlier: 6.259A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL H 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL I 350 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL J 350 " --> pdb=" O GLN K 351 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL K 350 " --> pdb=" O GLN L 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 354 through 356 removed outlier: 8.445A pdb=" N ILE G 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ILE H 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE I 354 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE J 354 " --> pdb=" O GLY K 355 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE K 354 " --> pdb=" O GLY L 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 359 through 362 removed outlier: 6.474A pdb=" N ASN G 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS H 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN H 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS I 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR H 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN I 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N HIS J 362 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR I 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN J 359 " --> pdb=" O ILE K 360 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS K 362 " --> pdb=" O ASN J 359 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR J 361 " --> pdb=" O HIS K 362 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN K 359 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS L 362 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR K 361 " --> pdb=" O HIS L 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 365 through 366 removed outlier: 4.205A pdb=" N GLY G 365 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY H 365 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY I 365 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY J 365 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY K 365 " --> pdb=" O GLY L 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 369 through 377 180 hydrogen bonds defined for protein. 540 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: 0.71 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2208 1.34 - 1.46: 1082 1.46 - 1.57: 3562 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 6864 Sorted by residual: bond pdb=" N GLU G 338 " pdb=" CA GLU G 338 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.22e-02 6.72e+03 5.30e+00 bond pdb=" N GLU E 338 " pdb=" CA GLU E 338 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.22e-02 6.72e+03 4.91e+00 bond pdb=" N GLU B 338 " pdb=" CA GLU B 338 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.22e-02 6.72e+03 4.76e+00 bond pdb=" N GLU J 338 " pdb=" CA GLU J 338 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.22e-02 6.72e+03 4.69e+00 bond pdb=" N GLU K 338 " pdb=" CA GLU K 338 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.22e-02 6.72e+03 4.63e+00 ... (remaining 6859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 8613 1.29 - 2.57: 386 2.57 - 3.86: 133 3.86 - 5.15: 36 5.15 - 6.43: 24 Bond angle restraints: 9192 Sorted by residual: angle pdb=" CA LYS F 311 " pdb=" CB LYS F 311 " pdb=" CG LYS F 311 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA LYS G 311 " pdb=" CB LYS G 311 " pdb=" CG LYS G 311 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA LYS L 311 " pdb=" CB LYS L 311 " pdb=" CG LYS L 311 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " pdb=" CG LYS D 311 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA LYS C 311 " pdb=" CB LYS C 311 " pdb=" CG LYS C 311 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 ... (remaining 9187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3875 17.45 - 34.89: 289 34.89 - 52.34: 0 52.34 - 69.79: 6 69.79 - 87.23: 6 Dihedral angle restraints: 4176 sinusoidal: 1728 harmonic: 2448 Sorted by residual: dihedral pdb=" CA GLY D 365 " pdb=" C GLY D 365 " pdb=" N GLY D 366 " pdb=" CA GLY D 366 " ideal model delta harmonic sigma weight residual 180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLY J 365 " pdb=" C GLY J 365 " pdb=" N GLY J 366 " pdb=" CA GLY J 366 " ideal model delta harmonic sigma weight residual -180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLY H 365 " pdb=" C GLY H 365 " pdb=" N GLY H 366 " pdb=" CA GLY H 366 " ideal model delta harmonic sigma weight residual 180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 528 0.027 - 0.053: 225 0.053 - 0.080: 97 0.080 - 0.107: 103 0.107 - 0.133: 91 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CA ILE I 328 " pdb=" N ILE I 328 " pdb=" C ILE I 328 " pdb=" CB ILE I 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE L 328 " pdb=" N ILE L 328 " pdb=" C ILE L 328 " pdb=" CB ILE L 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE K 328 " pdb=" N ILE K 328 " pdb=" C ILE K 328 " pdb=" CB ILE K 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1041 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO G 364 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 363 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO I 364 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 364 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 364 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 364 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.022 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 3523 3.02 - 3.49: 6159 3.49 - 3.96: 10762 3.96 - 4.43: 11315 4.43 - 4.90: 23763 Nonbonded interactions: 55522 Sorted by model distance: nonbonded pdb=" N ASN F 327 " pdb=" OD1 ASN F 327 " model vdw 2.546 3.120 nonbonded pdb=" N ASN H 327 " pdb=" OD1 ASN H 327 " model vdw 2.546 3.120 nonbonded pdb=" N ASN G 327 " pdb=" OD1 ASN G 327 " model vdw 2.546 3.120 nonbonded pdb=" N ASN I 327 " pdb=" OD1 ASN I 327 " model vdw 2.546 3.120 nonbonded pdb=" N ASN L 327 " pdb=" OD1 ASN L 327 " model vdw 2.546 3.120 ... (remaining 55517 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.004 0.028 6864 Z= 0.185 Angle : 0.789 6.433 9192 Z= 0.393 Chirality : 0.053 0.133 1044 Planarity : 0.006 0.039 1164 Dihedral : 11.833 87.232 2616 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.006 0.002 TYR J 310 PHE 0.004 0.001 PHE L 346 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6864) covalent geometry : angle 0.78923 ( 9192) hydrogen bonds : bond 0.14829 ( 180) hydrogen bonds : angle 5.74361 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.259 Fit side-chains REVERT: B 349 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7143 (mtp180) REVERT: C 343 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8200 (mptp) REVERT: E 340 LYS cc_start: 0.8635 (mttm) cc_final: 0.8383 (mptt) REVERT: G 340 LYS cc_start: 0.8785 (mttm) cc_final: 0.8328 (mttp) REVERT: K 349 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.7164 (mtp180) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.6891 time to fit residues: 176.9886 Evaluate side-chains 127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN F 351 GLN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 ASN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.137852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099845 restraints weight = 7177.416| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.77 r_work: 0.3612 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 6864 Z= 0.284 Angle : 0.886 6.859 9192 Z= 0.442 Chirality : 0.055 0.155 1044 Planarity : 0.005 0.046 1164 Dihedral : 6.352 21.768 900 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.92 % Allowed : 16.54 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG L 349 TYR 0.015 0.004 TYR H 310 PHE 0.005 0.001 PHE G 346 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00674 ( 6864) covalent geometry : angle 0.88560 ( 9192) hydrogen bonds : bond 0.05425 ( 180) hydrogen bonds : angle 4.54565 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.270 Fit side-chains REVERT: C 342 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7938 (mm-30) REVERT: E 342 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7944 (mm-30) REVERT: E 349 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: F 311 LYS cc_start: 0.8663 (mptt) cc_final: 0.8310 (mptt) REVERT: F 349 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7222 (mtp180) REVERT: H 342 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7831 (mm-30) REVERT: J 349 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7103 (mtm-85) REVERT: K 349 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7034 (mtp180) outliers start: 15 outliers final: 11 residues processed: 180 average time/residue: 0.5084 time to fit residues: 95.4886 Evaluate side-chains 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN ** L 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.138571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100808 restraints weight = 7140.243| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.76 r_work: 0.3633 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6864 Z= 0.223 Angle : 0.784 6.681 9192 Z= 0.387 Chirality : 0.053 0.144 1044 Planarity : 0.005 0.047 1164 Dihedral : 6.165 21.067 900 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.33 % Allowed : 15.51 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 349 TYR 0.013 0.003 TYR K 310 PHE 0.004 0.001 PHE I 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 6864) covalent geometry : angle 0.78426 ( 9192) hydrogen bonds : bond 0.04563 ( 180) hydrogen bonds : angle 4.55204 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.241 Fit side-chains REVERT: E 342 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 349 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7260 (mpp-170) REVERT: G 311 LYS cc_start: 0.8774 (mptt) cc_final: 0.7698 (ttpp) REVERT: H 342 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7875 (mm-30) REVERT: J 349 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7134 (mtm-85) REVERT: K 349 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.7042 (mtp180) REVERT: L 311 LYS cc_start: 0.7020 (mptp) cc_final: 0.6791 (mttm) REVERT: L 349 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7483 (mtm-85) outliers start: 26 outliers final: 13 residues processed: 174 average time/residue: 0.5626 time to fit residues: 102.2132 Evaluate side-chains 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.140148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102748 restraints weight = 7205.996| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.76 r_work: 0.3665 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6864 Z= 0.154 Angle : 0.708 7.026 9192 Z= 0.342 Chirality : 0.051 0.134 1044 Planarity : 0.004 0.047 1164 Dihedral : 5.823 19.018 900 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.21 % Allowed : 17.69 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG I 349 TYR 0.010 0.003 TYR K 310 PHE 0.004 0.001 PHE J 346 HIS 0.002 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6864) covalent geometry : angle 0.70807 ( 9192) hydrogen bonds : bond 0.03653 ( 180) hydrogen bonds : angle 4.45260 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.276 Fit side-chains REVERT: A 342 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7752 (mp0) REVERT: B 349 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7219 (mtm180) REVERT: E 342 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7897 (mm-30) REVERT: E 349 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7218 (mpp-170) REVERT: F 349 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7146 (mtp180) REVERT: G 311 LYS cc_start: 0.8736 (mptt) cc_final: 0.7737 (ttpp) REVERT: J 349 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7106 (mtm-85) REVERT: K 349 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7047 (mtp180) REVERT: L 311 LYS cc_start: 0.6643 (mptp) cc_final: 0.6418 (mttm) outliers start: 25 outliers final: 17 residues processed: 157 average time/residue: 0.4674 time to fit residues: 77.0191 Evaluate side-chains 149 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 0.0670 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 3.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 359 ASN D 359 ASN E 359 ASN F 359 ASN H 359 ASN I 359 ASN J 359 ASN K 359 ASN L 359 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.138779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.101306 restraints weight = 7199.366| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.75 r_work: 0.3642 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6864 Z= 0.204 Angle : 0.747 7.728 9192 Z= 0.363 Chirality : 0.051 0.140 1044 Planarity : 0.004 0.047 1164 Dihedral : 6.022 20.702 900 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.72 % Allowed : 18.33 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG L 349 TYR 0.015 0.004 TYR J 310 PHE 0.004 0.001 PHE J 346 HIS 0.002 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 6864) covalent geometry : angle 0.74745 ( 9192) hydrogen bonds : bond 0.04146 ( 180) hydrogen bonds : angle 4.56884 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.234 Fit side-chains REVERT: A 342 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7803 (mp0) REVERT: B 349 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7199 (mtm180) REVERT: E 342 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7932 (mm-30) REVERT: F 349 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7149 (mtp180) REVERT: J 349 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7073 (mtm-85) REVERT: L 311 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6215 (mmpt) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.5212 time to fit residues: 85.5934 Evaluate side-chains 151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.138627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.100348 restraints weight = 7342.630| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.78 r_work: 0.3620 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6864 Z= 0.283 Angle : 0.815 8.120 9192 Z= 0.401 Chirality : 0.054 0.146 1044 Planarity : 0.005 0.053 1164 Dihedral : 6.320 22.980 900 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.08 % Allowed : 18.85 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG L 349 TYR 0.020 0.005 TYR F 310 PHE 0.005 0.001 PHE I 346 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 6864) covalent geometry : angle 0.81455 ( 9192) hydrogen bonds : bond 0.04750 ( 180) hydrogen bonds : angle 4.66385 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.267 Fit side-chains REVERT: A 342 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7824 (mp0) REVERT: E 342 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7979 (mm-30) REVERT: E 349 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7227 (mpp-170) REVERT: G 311 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: K 349 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7141 (mtp180) REVERT: L 311 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5757 (mmpt) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.4368 time to fit residues: 69.4620 Evaluate side-chains 150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.138932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101594 restraints weight = 7147.092| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.74 r_work: 0.3646 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6864 Z= 0.197 Angle : 0.739 7.926 9192 Z= 0.359 Chirality : 0.051 0.136 1044 Planarity : 0.005 0.049 1164 Dihedral : 6.058 21.438 900 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.33 % Allowed : 18.46 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.003 ARG F 349 TYR 0.014 0.003 TYR F 310 PHE 0.005 0.001 PHE L 378 HIS 0.002 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6864) covalent geometry : angle 0.73911 ( 9192) hydrogen bonds : bond 0.04017 ( 180) hydrogen bonds : angle 4.55856 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.253 Fit side-chains REVERT: A 342 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7815 (mp0) REVERT: B 349 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7221 (mtm180) REVERT: E 342 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7939 (mm-30) REVERT: E 349 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7337 (mpp-170) REVERT: F 349 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7104 (mtp180) REVERT: G 311 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8052 (ttpp) REVERT: J 349 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7105 (mtm-85) REVERT: K 349 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7141 (mtp180) REVERT: L 311 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5405 (mmpt) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.4742 time to fit residues: 78.5134 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN L 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.138529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.101075 restraints weight = 7199.015| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.75 r_work: 0.3642 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6864 Z= 0.214 Angle : 0.761 8.662 9192 Z= 0.368 Chirality : 0.052 0.140 1044 Planarity : 0.005 0.054 1164 Dihedral : 6.122 21.718 900 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.95 % Allowed : 19.49 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG L 349 TYR 0.016 0.004 TYR F 310 PHE 0.005 0.001 PHE L 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 6864) covalent geometry : angle 0.76085 ( 9192) hydrogen bonds : bond 0.04189 ( 180) hydrogen bonds : angle 4.59205 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.276 Fit side-chains REVERT: A 342 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7792 (mp0) REVERT: E 342 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7945 (mm-30) REVERT: E 349 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7362 (mpp-170) REVERT: F 349 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7160 (mtp180) REVERT: G 311 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: J 349 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7059 (mtm-85) REVERT: K 349 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7264 (mpp-170) REVERT: L 311 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5178 (mmpt) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.4611 time to fit residues: 74.8986 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 329 HIS F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.140056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.102578 restraints weight = 7196.175| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.76 r_work: 0.3660 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6864 Z= 0.167 Angle : 0.728 8.698 9192 Z= 0.347 Chirality : 0.051 0.133 1044 Planarity : 0.005 0.052 1164 Dihedral : 5.888 20.519 900 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.69 % Allowed : 20.64 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.26), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG L 349 TYR 0.012 0.003 TYR F 310 PHE 0.004 0.001 PHE L 378 HIS 0.002 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6864) covalent geometry : angle 0.72778 ( 9192) hydrogen bonds : bond 0.03708 ( 180) hydrogen bonds : angle 4.50454 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.165 Fit side-chains REVERT: A 342 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7793 (mp0) REVERT: B 349 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7244 (mtm180) REVERT: E 342 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7950 (mm-30) REVERT: E 349 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7362 (mpp-170) REVERT: F 349 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7150 (mtp180) REVERT: G 311 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7981 (ttpp) REVERT: J 349 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7060 (mtm-85) REVERT: K 349 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7277 (mpp-170) REVERT: L 311 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5390 (mmpt) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.4745 time to fit residues: 76.4067 Evaluate side-chains 155 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 7 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.140453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.102941 restraints weight = 7149.544| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.76 r_work: 0.3665 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6864 Z= 0.159 Angle : 0.730 9.172 9192 Z= 0.346 Chirality : 0.050 0.132 1044 Planarity : 0.004 0.054 1164 Dihedral : 5.801 19.881 900 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.56 % Allowed : 20.77 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG L 349 TYR 0.012 0.003 TYR K 310 PHE 0.004 0.001 PHE L 378 HIS 0.002 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6864) covalent geometry : angle 0.73015 ( 9192) hydrogen bonds : bond 0.03606 ( 180) hydrogen bonds : angle 4.47079 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.205 Fit side-chains REVERT: A 342 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7790 (mp0) REVERT: C 343 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7881 (mptp) REVERT: E 342 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7932 (mm-30) REVERT: E 349 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7374 (mpp-170) REVERT: F 349 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7151 (mtp180) REVERT: G 311 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7889 (ttpp) REVERT: J 349 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7066 (mtm-85) REVERT: K 349 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7229 (mpp-170) REVERT: L 311 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5038 (mttm) REVERT: L 349 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7511 (mtm-85) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 0.5160 time to fit residues: 82.2404 Evaluate side-chains 153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.142739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.105548 restraints weight = 7198.657| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.76 r_work: 0.3707 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6864 Z= 0.117 Angle : 0.688 9.160 9192 Z= 0.321 Chirality : 0.050 0.127 1044 Planarity : 0.004 0.058 1164 Dihedral : 5.451 17.387 900 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.31 % Allowed : 21.41 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.25), residues: 864 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG L 349 TYR 0.008 0.002 TYR K 310 PHE 0.004 0.001 PHE J 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6864) covalent geometry : angle 0.68815 ( 9192) hydrogen bonds : bond 0.02927 ( 180) hydrogen bonds : angle 4.33962 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.35 seconds wall clock time: 51 minutes 30.05 seconds (3090.05 seconds total)