Starting phenix.real_space_refine on Sun Apr 5 16:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.map" model { file = "/net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlo_22375/04_2026/7jlo_22375.cif" } resolution = 3.4 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= 0.001 sd= 0.009 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 69 5.16 5 C 7881 2.51 5 N 2022 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11964 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.51, per 1000 atoms: 0.21 Number of scatterers: 11964 At special positions: 0 Unit cell: (129.276, 123.606, 88.452, 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 69 16.00 O 1992 8.00 N 2022 7.00 C 7881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " 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: 0.96 Conformation dependent library (CDL) restraints added in 404.7 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 72.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 58 through 86 Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.934A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 300 Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.559A pdb=" N MET A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU A 437 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 481 through 492 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 58 through 86 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.935A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 300 Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.880A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 406 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 472 through 481 Processing helix chain 'B' and resid 481 through 492 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 58 through 86 Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.933A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 300 Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.590A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU C 437 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.524A pdb=" N TRP C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 481 through 492 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 699 hydrogen bonds defined for protein. 2025 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: 1.44 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3759 1.34 - 1.46: 3117 1.46 - 1.58: 5331 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12300 Sorted by residual: bond pdb=" C HIS A 451 " pdb=" N TRP A 452 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.12e+00 bond pdb=" C HIS B 451 " pdb=" N TRP B 452 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C HIS C 451 " pdb=" N TRP C 452 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.82e-01 bond pdb=" C TYR C 152 " pdb=" O TYR C 152 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.45e-01 bond pdb=" CB GLU C 399 " pdb=" CG GLU C 399 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 12295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 15593 1.07 - 2.14: 937 2.14 - 3.21: 114 3.21 - 4.28: 39 4.28 - 5.35: 24 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N GLN C 528 " pdb=" CA GLN C 528 " pdb=" C GLN C 528 " ideal model delta sigma weight residual 111.02 115.45 -4.43 1.22e+00 6.72e-01 1.32e+01 angle pdb=" N GLN B 528 " pdb=" CA GLN B 528 " pdb=" C GLN B 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N GLN A 528 " pdb=" CA GLN A 528 " pdb=" C GLN A 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N ARG C 527 " pdb=" CA ARG C 527 " pdb=" C ARG C 527 " ideal model delta sigma weight residual 109.96 105.28 4.68 1.68e+00 3.54e-01 7.77e+00 angle pdb=" N ARG B 527 " pdb=" CA ARG B 527 " pdb=" C ARG B 527 " ideal model delta sigma weight residual 109.96 105.30 4.66 1.68e+00 3.54e-01 7.69e+00 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6455 17.83 - 35.67: 573 35.67 - 53.50: 112 53.50 - 71.33: 30 71.33 - 89.17: 12 Dihedral angle restraints: 7182 sinusoidal: 2904 harmonic: 4278 Sorted by residual: dihedral pdb=" CA ARG B 527 " pdb=" C ARG B 527 " pdb=" N GLN B 528 " pdb=" CA GLN B 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG C 527 " pdb=" C ARG C 527 " pdb=" N GLN C 528 " pdb=" CA GLN C 528 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 846 0.024 - 0.047: 542 0.047 - 0.071: 328 0.071 - 0.095: 86 0.095 - 0.118: 67 Chirality restraints: 1869 Sorted by residual: chirality pdb=" CA ILE C 170 " pdb=" N ILE C 170 " pdb=" C ILE C 170 " pdb=" CB ILE C 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 170 " pdb=" N ILE B 170 " pdb=" C ILE B 170 " pdb=" CB ILE B 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 1866 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 117 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 117 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 117 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.017 5.00e-02 4.00e+02 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1152 2.74 - 3.28: 11901 3.28 - 3.82: 19337 3.82 - 4.36: 22439 4.36 - 4.90: 39499 Nonbonded interactions: 94328 Sorted by model distance: nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.203 3.040 nonbonded pdb=" O HIS B 406 " pdb=" OG1 THR B 410 " model vdw 2.203 3.040 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.230 3.120 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.231 3.120 ... (remaining 94323 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.450 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.031 12303 Z= 0.198 Angle : 0.604 5.350 16713 Z= 0.361 Chirality : 0.041 0.118 1869 Planarity : 0.003 0.031 2085 Dihedral : 14.679 89.167 4401 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.46 % Allowed : 5.03 % Favored : 94.51 % 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: -2.15 (0.20), residues: 1443 helix: -0.55 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -3.14 (0.21), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 495 TYR 0.012 0.001 TYR B 152 PHE 0.018 0.001 PHE C 79 TRP 0.010 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00443 (12300) covalent geometry : angle 0.60289 (16707) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.67656 ( 6) hydrogen bonds : bond 0.11522 ( 699) hydrogen bonds : angle 5.04083 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.421 Fit side-chains REVERT: A 62 MET cc_start: 0.8289 (ttp) cc_final: 0.7877 (ttp) REVERT: A 69 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 422 ARG cc_start: 0.7614 (tpt-90) cc_final: 0.7265 (mmm160) REVERT: B 69 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 125 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8004 (ttm110) REVERT: B 159 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 372 LEU cc_start: 0.8587 (tp) cc_final: 0.8379 (tp) REVERT: B 427 ASP cc_start: 0.8598 (p0) cc_final: 0.8355 (p0) REVERT: C 89 TYR cc_start: 0.8861 (m-80) cc_final: 0.8585 (m-80) outliers start: 6 outliers final: 2 residues processed: 209 average time/residue: 0.1284 time to fit residues: 35.9971 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 342 HIS A 451 HIS A 467 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 342 HIS B 428 GLN B 451 HIS B 467 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 210 HIS C 342 HIS C 451 HIS C 467 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093715 restraints weight = 16410.881| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.83 r_work: 0.2834 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12303 Z= 0.137 Angle : 0.512 5.315 16713 Z= 0.268 Chirality : 0.039 0.119 1869 Planarity : 0.004 0.056 2085 Dihedral : 4.516 23.457 1595 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.85 % Allowed : 11.14 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.22), residues: 1443 helix: 0.62 (0.17), residues: 957 sheet: -1.24 (0.85), residues: 30 loop : -2.50 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 125 TYR 0.017 0.001 TYR A 152 PHE 0.012 0.001 PHE A 79 TRP 0.010 0.001 TRP B 180 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00321 (12300) covalent geometry : angle 0.51160 (16707) SS BOND : bond 0.00049 ( 3) SS BOND : angle 1.09886 ( 6) hydrogen bonds : bond 0.04604 ( 699) hydrogen bonds : angle 3.82570 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.317 Fit side-chains REVERT: A 62 MET cc_start: 0.8636 (ttp) cc_final: 0.8377 (ttp) REVERT: A 69 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 300 LEU cc_start: 0.8562 (mm) cc_final: 0.8326 (mt) REVERT: A 422 ARG cc_start: 0.8418 (tpt-90) cc_final: 0.8083 (mmp80) REVERT: B 51 TYR cc_start: 0.9418 (t80) cc_final: 0.8726 (t80) REVERT: B 125 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.7960 (ttm110) REVERT: B 146 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8260 (mtm110) REVERT: B 159 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 422 ARG cc_start: 0.8406 (mmm160) cc_final: 0.7727 (mmp80) REVERT: C 159 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 524 MET cc_start: 0.5665 (ptp) cc_final: 0.5433 (pmm) outliers start: 11 outliers final: 10 residues processed: 144 average time/residue: 0.1283 time to fit residues: 25.2955 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096701 restraints weight = 16336.423| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.81 r_work: 0.2865 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12303 Z= 0.101 Angle : 0.462 6.611 16713 Z= 0.241 Chirality : 0.037 0.122 1869 Planarity : 0.003 0.056 2085 Dihedral : 4.190 21.075 1593 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.39 % Allowed : 13.23 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1443 helix: 1.21 (0.18), residues: 936 sheet: -1.19 (0.87), residues: 30 loop : -2.06 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 125 TYR 0.015 0.001 TYR A 152 PHE 0.009 0.001 PHE A 469 TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00214 (12300) covalent geometry : angle 0.46166 (16707) SS BOND : bond 0.00025 ( 3) SS BOND : angle 0.86770 ( 6) hydrogen bonds : bond 0.03998 ( 699) hydrogen bonds : angle 3.58007 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.475 Fit side-chains REVERT: A 62 MET cc_start: 0.8453 (ttp) cc_final: 0.8198 (ttp) REVERT: A 69 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 422 ARG cc_start: 0.8343 (tpt-90) cc_final: 0.7993 (mmp80) REVERT: B 51 TYR cc_start: 0.9383 (t80) cc_final: 0.8947 (t80) REVERT: B 125 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.7974 (ttm110) REVERT: B 146 ARG cc_start: 0.8510 (mtm180) cc_final: 0.8193 (mtm110) REVERT: B 159 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 396 ILE cc_start: 0.8606 (mt) cc_final: 0.8342 (mm) outliers start: 18 outliers final: 16 residues processed: 138 average time/residue: 0.1257 time to fit residues: 24.3489 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 379 ASN B 57 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 379 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 379 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.091589 restraints weight = 16684.140| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.77 r_work: 0.2787 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12303 Z= 0.224 Angle : 0.555 6.467 16713 Z= 0.288 Chirality : 0.042 0.186 1869 Planarity : 0.004 0.041 2085 Dihedral : 4.564 22.184 1593 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.63 % Allowed : 13.23 % Favored : 84.15 % 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: -0.07 (0.22), residues: 1443 helix: 1.00 (0.18), residues: 957 sheet: None (None), residues: 0 loop : -2.23 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.016 0.001 TYR A 152 PHE 0.016 0.001 PHE B 79 TRP 0.011 0.001 TRP B 180 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00548 (12300) covalent geometry : angle 0.55445 (16707) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.80703 ( 6) hydrogen bonds : bond 0.05267 ( 699) hydrogen bonds : angle 3.82958 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.384 Fit side-chains REVERT: A 69 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 422 ARG cc_start: 0.8372 (tpt-90) cc_final: 0.8085 (mmp80) REVERT: B 125 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.7974 (ttm110) REVERT: B 159 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 422 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7924 (tpp-160) REVERT: C 159 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8342 (tm-30) outliers start: 34 outliers final: 28 residues processed: 156 average time/residue: 0.1051 time to fit residues: 23.7974 Evaluate side-chains 149 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 224 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096643 restraints weight = 16440.431| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.73 r_work: 0.2823 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12303 Z= 0.105 Angle : 0.460 5.726 16713 Z= 0.242 Chirality : 0.037 0.118 1869 Planarity : 0.003 0.040 2085 Dihedral : 4.254 20.312 1593 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.86 % Allowed : 14.62 % Favored : 83.53 % 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: 0.45 (0.23), residues: 1443 helix: 1.35 (0.18), residues: 939 sheet: -1.19 (0.89), residues: 30 loop : -1.77 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.014 0.001 TYR A 152 PHE 0.009 0.001 PHE B 469 TRP 0.007 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00225 (12300) covalent geometry : angle 0.45938 (16707) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.80263 ( 6) hydrogen bonds : bond 0.04122 ( 699) hydrogen bonds : angle 3.56565 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.438 Fit side-chains REVERT: A 69 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8443 (mm-30) REVERT: A 422 ARG cc_start: 0.8255 (tpt-90) cc_final: 0.7958 (mmp80) REVERT: B 51 TYR cc_start: 0.9384 (t80) cc_final: 0.8948 (t80) REVERT: B 125 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7958 (ttm110) REVERT: B 146 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8256 (mtm110) REVERT: B 159 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 422 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7804 (tpp-160) REVERT: C 159 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8305 (tm-30) REVERT: C 422 ARG cc_start: 0.8681 (mmt90) cc_final: 0.8189 (mtp85) outliers start: 24 outliers final: 21 residues processed: 141 average time/residue: 0.1109 time to fit residues: 22.3706 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.094221 restraints weight = 16601.108| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.82 r_work: 0.2796 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12303 Z= 0.166 Angle : 0.498 5.698 16713 Z= 0.261 Chirality : 0.039 0.116 1869 Planarity : 0.004 0.041 2085 Dihedral : 4.373 19.866 1593 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.86 % Allowed : 15.62 % Favored : 82.52 % 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: 0.45 (0.23), residues: 1443 helix: 1.31 (0.18), residues: 942 sheet: -1.16 (0.90), residues: 30 loop : -1.73 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 527 TYR 0.015 0.001 TYR A 152 PHE 0.011 0.001 PHE B 79 TRP 0.009 0.001 TRP B 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00403 (12300) covalent geometry : angle 0.49798 (16707) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.74955 ( 6) hydrogen bonds : bond 0.04714 ( 699) hydrogen bonds : angle 3.65736 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.372 Fit side-chains REVERT: A 69 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8584 (mm-30) REVERT: A 422 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.8082 (mmp80) REVERT: A 448 MET cc_start: 0.8208 (mtp) cc_final: 0.7943 (mtt) REVERT: B 51 TYR cc_start: 0.9414 (t80) cc_final: 0.8804 (t80) REVERT: B 125 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.7980 (ttm110) REVERT: B 146 ARG cc_start: 0.8544 (mtm180) cc_final: 0.8297 (mtm110) REVERT: B 159 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 320 LEU cc_start: 0.8468 (mm) cc_final: 0.8090 (mp) REVERT: B 422 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7920 (tpp-160) REVERT: C 159 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 422 ARG cc_start: 0.8677 (mmt90) cc_final: 0.8191 (mtp85) outliers start: 24 outliers final: 23 residues processed: 141 average time/residue: 0.1131 time to fit residues: 22.6322 Evaluate side-chains 138 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.098322 restraints weight = 16312.263| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.79 r_work: 0.2854 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12303 Z= 0.099 Angle : 0.451 8.090 16713 Z= 0.235 Chirality : 0.037 0.118 1869 Planarity : 0.003 0.042 2085 Dihedral : 4.140 19.061 1593 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.78 % Allowed : 16.24 % Favored : 81.98 % 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: 0.67 (0.23), residues: 1443 helix: 1.52 (0.18), residues: 930 sheet: -1.24 (0.89), residues: 30 loop : -1.62 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.014 0.001 TYR A 152 PHE 0.009 0.001 PHE B 469 TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00209 (12300) covalent geometry : angle 0.45134 (16707) SS BOND : bond 0.00055 ( 3) SS BOND : angle 0.69022 ( 6) hydrogen bonds : bond 0.03973 ( 699) hydrogen bonds : angle 3.49014 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.446 Fit side-chains REVERT: A 69 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8505 (mm-30) REVERT: A 422 ARG cc_start: 0.8284 (tpt-90) cc_final: 0.7996 (mmp80) REVERT: A 448 MET cc_start: 0.8152 (mtp) cc_final: 0.7784 (mtm) REVERT: B 51 TYR cc_start: 0.9358 (t80) cc_final: 0.9059 (t80) REVERT: B 125 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.7956 (ttm110) REVERT: B 146 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8271 (mtm110) REVERT: B 159 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8215 (tm-30) REVERT: C 159 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 422 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8206 (mtp85) outliers start: 23 outliers final: 19 residues processed: 141 average time/residue: 0.1067 time to fit residues: 21.7886 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098830 restraints weight = 16320.263| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.71 r_work: 0.2892 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12303 Z= 0.098 Angle : 0.447 8.201 16713 Z= 0.233 Chirality : 0.037 0.117 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.085 17.816 1593 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 16.78 % Favored : 81.67 % 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: 0.78 (0.23), residues: 1443 helix: 1.59 (0.18), residues: 930 sheet: -1.24 (0.90), residues: 30 loop : -1.54 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.014 0.001 TYR A 152 PHE 0.009 0.001 PHE A 469 TRP 0.008 0.001 TRP C 180 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00209 (12300) covalent geometry : angle 0.44706 (16707) SS BOND : bond 0.00063 ( 3) SS BOND : angle 0.63993 ( 6) hydrogen bonds : bond 0.03915 ( 699) hydrogen bonds : angle 3.46287 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.448 Fit side-chains REVERT: A 69 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8504 (mm-30) REVERT: A 89 TYR cc_start: 0.8821 (m-80) cc_final: 0.8614 (m-80) REVERT: A 422 ARG cc_start: 0.8252 (tpt-90) cc_final: 0.7979 (mmp80) REVERT: B 125 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.7965 (ttm110) REVERT: B 146 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8240 (mtm110) REVERT: B 159 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 159 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 422 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8179 (mtp85) outliers start: 20 outliers final: 17 residues processed: 132 average time/residue: 0.1108 time to fit residues: 20.9446 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100945 restraints weight = 16155.049| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.76 r_work: 0.2872 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12303 Z= 0.112 Angle : 0.463 7.740 16713 Z= 0.240 Chirality : 0.038 0.118 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.114 18.109 1593 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 17.01 % Favored : 81.44 % 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: 0.80 (0.23), residues: 1443 helix: 1.60 (0.18), residues: 930 sheet: -1.24 (0.91), residues: 30 loop : -1.50 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.014 0.001 TYR A 152 PHE 0.008 0.001 PHE B 469 TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00255 (12300) covalent geometry : angle 0.46246 (16707) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.60523 ( 6) hydrogen bonds : bond 0.04068 ( 699) hydrogen bonds : angle 3.49301 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.442 Fit side-chains REVERT: A 69 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 422 ARG cc_start: 0.8347 (tpt-90) cc_final: 0.8087 (mmp80) REVERT: B 125 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7951 (ttm110) REVERT: B 146 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8242 (mtm110) REVERT: B 159 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 159 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 422 ARG cc_start: 0.8660 (mmt90) cc_final: 0.8174 (mtp85) outliers start: 20 outliers final: 19 residues processed: 131 average time/residue: 0.1134 time to fit residues: 21.2422 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** 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 = 0.3327 r_free = 0.3327 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100146 restraints weight = 16411.749| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.78 r_work: 0.2866 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12303 Z= 0.114 Angle : 0.465 7.589 16713 Z= 0.241 Chirality : 0.038 0.117 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.121 18.234 1593 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.62 % Allowed : 17.17 % Favored : 81.21 % 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: 0.82 (0.23), residues: 1443 helix: 1.61 (0.18), residues: 930 sheet: -1.25 (0.91), residues: 30 loop : -1.49 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.015 0.001 TYR B 51 PHE 0.008 0.001 PHE A 469 TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00260 (12300) covalent geometry : angle 0.46488 (16707) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.60109 ( 6) hydrogen bonds : bond 0.04116 ( 699) hydrogen bonds : angle 3.49549 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.461 Fit side-chains REVERT: A 69 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8539 (mm-30) REVERT: A 422 ARG cc_start: 0.8351 (tpt-90) cc_final: 0.8091 (mmp80) REVERT: B 125 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7954 (ttm110) REVERT: B 146 ARG cc_start: 0.8501 (mtm180) cc_final: 0.8255 (mtm110) REVERT: B 159 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 159 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 422 ARG cc_start: 0.8683 (mmt90) cc_final: 0.8192 (mtp85) outliers start: 21 outliers final: 20 residues processed: 131 average time/residue: 0.1194 time to fit residues: 21.9735 Evaluate side-chains 132 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 137 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097067 restraints weight = 16332.547| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.82 r_work: 0.2884 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12303 Z= 0.099 Angle : 0.452 7.709 16713 Z= 0.234 Chirality : 0.037 0.117 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.044 17.555 1593 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.62 % Allowed : 17.25 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1443 helix: 1.67 (0.18), residues: 930 sheet: -1.27 (0.90), residues: 30 loop : -1.47 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.014 0.001 TYR A 152 PHE 0.009 0.001 PHE A 469 TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00217 (12300) covalent geometry : angle 0.45149 (16707) SS BOND : bond 0.00061 ( 3) SS BOND : angle 0.59242 ( 6) hydrogen bonds : bond 0.03871 ( 699) hydrogen bonds : angle 3.45011 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.02 seconds wall clock time: 45 minutes 17.97 seconds (2717.97 seconds total)