Starting phenix.real_space_refine on Sat Aug 23 00:28:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3d_35150/08_2025/8i3d_35150.cif" } resolution = 2.81 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= 0.107 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 58 5.16 5 C 5720 2.51 5 N 1474 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8798 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4399 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 3.35, per 1000 atoms: 0.38 Number of scatterers: 8798 At special positions: 0 Unit cell: (75.53, 100.43, 123.67, 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 58 16.00 O 1546 8.00 N 1474 7.00 C 5720 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: 0.66 Conformation dependent library (CDL) restraints added in 438.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 59.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.574A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.631A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.584A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.543A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.706A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.529A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.632A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 removed outlier: 3.611A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 401 removed outlier: 3.676A pdb=" N CYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.707A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.696A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.532A pdb=" N GLN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.906A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.560A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.719A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 561 removed outlier: 3.640A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.000A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.558A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.060A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.705A pdb=" N VAL A 625 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 659 removed outlier: 3.881A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.574A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.631A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.586A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.542A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.705A pdb=" N PHE B 275 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.529A pdb=" N LEU B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.632A pdb=" N THR B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.611A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 401 removed outlier: 3.677A pdb=" N CYS B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.707A pdb=" N SER B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.697A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.531A pdb=" N GLN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.906A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.559A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.719A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.640A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 4.001A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.558A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.060A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 removed outlier: 3.705A pdb=" N VAL B 625 " --> pdb=" O CYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 659 removed outlier: 3.881A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 6.221A pdb=" N TYR A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 85 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 45 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 87 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 43 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 89 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 41 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 45 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 124 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.622A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 91 removed outlier: 6.222A pdb=" N TYR B 47 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 85 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 45 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 87 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 43 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B 89 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS B 41 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 45 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 124 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.623A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1302 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: 1.37 Time building geometry restraints manager: 0.91 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: 2698 1.34 - 1.46: 1713 1.46 - 1.57: 4477 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8980 Sorted by residual: bond pdb=" C ALA B 350 " pdb=" N PRO B 351 " ideal model delta sigma weight residual 1.335 1.372 -0.036 1.36e-02 5.41e+03 7.13e+00 bond pdb=" C ALA A 350 " pdb=" N PRO A 351 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 7.02e+00 bond pdb=" CB VAL B 507 " pdb=" CG1 VAL B 507 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.77e+00 bond pdb=" CB VAL A 507 " pdb=" CG1 VAL A 507 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.68e+00 bond pdb=" CB GLN B 531 " pdb=" CG GLN B 531 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 ... (remaining 8975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11563 1.98 - 3.95: 489 3.95 - 5.93: 66 5.93 - 7.90: 34 7.90 - 9.88: 14 Bond angle restraints: 12166 Sorted by residual: angle pdb=" C GLY B 605 " pdb=" N CYS B 606 " pdb=" CA CYS B 606 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C GLY A 605 " pdb=" N CYS A 606 " pdb=" CA CYS A 606 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C GLY B 597 " pdb=" N GLU B 598 " pdb=" CA GLU B 598 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY A 597 " pdb=" N GLU A 598 " pdb=" CA GLU A 598 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C CYS B 35 " pdb=" N PHE B 36 " pdb=" CA PHE B 36 " ideal model delta sigma weight residual 121.80 131.68 -9.88 2.44e+00 1.68e-01 1.64e+01 ... (remaining 12161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4619 15.12 - 30.24: 527 30.24 - 45.36: 104 45.36 - 60.48: 22 60.48 - 75.60: 8 Dihedral angle restraints: 5280 sinusoidal: 2046 harmonic: 3234 Sorted by residual: dihedral pdb=" CA GLY B 605 " pdb=" C GLY B 605 " pdb=" N CYS B 606 " pdb=" CA CYS B 606 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" N CYS A 606 " pdb=" CA CYS A 606 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N CYS B 286 " pdb=" CA CYS B 286 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 976 0.052 - 0.104: 382 0.104 - 0.156: 72 0.156 - 0.208: 12 0.208 - 0.260: 4 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CB VAL B 456 " pdb=" CA VAL B 456 " pdb=" CG1 VAL B 456 " pdb=" CG2 VAL B 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL A 456 " pdb=" CA VAL A 456 " pdb=" CG1 VAL A 456 " pdb=" CG2 VAL A 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE A 660 " pdb=" CA ILE A 660 " pdb=" CG1 ILE A 660 " pdb=" CG2 ILE A 660 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1443 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 350 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 351 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 351 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 495 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 496 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.034 5.00e-02 4.00e+02 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2948 2.84 - 3.36: 7482 3.36 - 3.87: 14139 3.87 - 4.39: 16962 4.39 - 4.90: 29567 Nonbonded interactions: 71098 Sorted by model distance: nonbonded pdb=" NH2 ARG B 436 " pdb=" O TYR B 508 " model vdw 2.328 3.120 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.329 3.040 nonbonded pdb=" NH2 ARG A 436 " pdb=" O TYR A 508 " model vdw 2.329 3.120 nonbonded pdb=" O SER A 85 " pdb=" OG SER A 85 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 452 " pdb=" O SER B 530 " model vdw 2.337 3.040 ... (remaining 71093 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' } 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: 2.570 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.070 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.009 0.086 8980 Z= 0.387 Angle : 0.993 9.880 12166 Z= 0.534 Chirality : 0.056 0.260 1446 Planarity : 0.007 0.064 1494 Dihedral : 13.502 75.601 3204 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.83 % Allowed : 4.99 % Favored : 94.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.74 (0.17), residues: 1112 helix: -4.53 (0.07), residues: 670 sheet: -0.75 (0.55), residues: 82 loop : -2.51 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 81 TYR 0.037 0.002 TYR A 475 PHE 0.021 0.002 PHE A 499 TRP 0.014 0.003 TRP A 425 HIS 0.009 0.002 HIS A 662 Details of bonding type rmsd covalent geometry : bond 0.00931 ( 8980) covalent geometry : angle 0.99324 (12166) hydrogen bonds : bond 0.29637 ( 446) hydrogen bonds : angle 10.05893 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 413 GLN cc_start: 0.8309 (tt0) cc_final: 0.7968 (mt0) REVERT: A 468 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7705 (ttm170) REVERT: B 174 THR cc_start: 0.8198 (m) cc_final: 0.7961 (p) REVERT: B 283 GLU cc_start: 0.6733 (pm20) cc_final: 0.6326 (mp0) REVERT: B 304 PHE cc_start: 0.8403 (m-80) cc_final: 0.8111 (m-80) REVERT: B 326 THR cc_start: 0.5791 (OUTLIER) cc_final: 0.5543 (t) REVERT: B 338 ARG cc_start: 0.8221 (ttp80) cc_final: 0.8014 (ttp80) REVERT: B 401 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7489 (mtp-110) REVERT: B 413 GLN cc_start: 0.8154 (tt0) cc_final: 0.7872 (mt0) REVERT: B 468 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7642 (ttm170) outliers start: 8 outliers final: 2 residues processed: 169 average time/residue: 0.7643 time to fit residues: 135.6043 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 266 GLN A 531 GLN B 224 ASN B 266 GLN B 311 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.157264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115563 restraints weight = 9130.294| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.74 r_work: 0.3040 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8980 Z= 0.124 Angle : 0.578 5.874 12166 Z= 0.303 Chirality : 0.040 0.127 1446 Planarity : 0.006 0.046 1494 Dihedral : 5.233 39.341 1227 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.33 % Allowed : 10.60 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.21), residues: 1112 helix: -2.03 (0.16), residues: 674 sheet: -0.38 (0.57), residues: 82 loop : -1.95 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 463 TYR 0.028 0.001 TYR A 475 PHE 0.009 0.001 PHE A 502 TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS A 662 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8980) covalent geometry : angle 0.57792 (12166) hydrogen bonds : bond 0.04349 ( 446) hydrogen bonds : angle 4.68666 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.424 Fit side-chains REVERT: A 273 GLN cc_start: 0.8136 (mm110) cc_final: 0.7792 (tp40) REVERT: A 274 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: A 346 ASP cc_start: 0.7334 (m-30) cc_final: 0.7100 (m-30) REVERT: A 413 GLN cc_start: 0.8530 (tt0) cc_final: 0.8282 (mt0) REVERT: A 468 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7284 (ttm170) REVERT: B 174 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.6859 (p) REVERT: B 183 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 247 GLN cc_start: 0.8204 (mt0) cc_final: 0.7940 (mt0) REVERT: B 256 LYS cc_start: 0.7989 (mttp) cc_final: 0.7737 (mttm) REVERT: B 283 GLU cc_start: 0.6951 (pm20) cc_final: 0.6505 (mp0) REVERT: B 314 ASP cc_start: 0.7928 (m-30) cc_final: 0.7710 (m-30) REVERT: B 468 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7159 (ttm170) outliers start: 32 outliers final: 7 residues processed: 157 average time/residue: 0.7433 time to fit residues: 122.9099 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 224 ASN A 247 GLN A 266 GLN B 154 HIS B 224 ASN B 266 GLN B 531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110327 restraints weight = 9082.375| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.88 r_work: 0.2982 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8980 Z= 0.212 Angle : 0.627 5.847 12166 Z= 0.322 Chirality : 0.044 0.139 1446 Planarity : 0.005 0.047 1494 Dihedral : 5.041 24.297 1226 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.01 % Allowed : 13.10 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.24), residues: 1112 helix: -0.70 (0.19), residues: 678 sheet: -0.15 (0.57), residues: 82 loop : -1.78 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 463 TYR 0.030 0.002 TYR A 475 PHE 0.021 0.002 PHE B 502 TRP 0.009 0.002 TRP A 447 HIS 0.007 0.001 HIS A 662 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8980) covalent geometry : angle 0.62702 (12166) hydrogen bonds : bond 0.04829 ( 446) hydrogen bonds : angle 4.39303 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.364 Fit side-chains REVERT: A 83 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 273 GLN cc_start: 0.8120 (mm110) cc_final: 0.7763 (tp40) REVERT: A 274 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: A 346 ASP cc_start: 0.7407 (m-30) cc_final: 0.7034 (m-30) REVERT: A 413 GLN cc_start: 0.8540 (tt0) cc_final: 0.8337 (mt0) REVERT: A 468 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7303 (ttm170) REVERT: A 565 TYR cc_start: 0.8823 (m-80) cc_final: 0.8607 (m-80) REVERT: A 603 MET cc_start: 0.7299 (mmt) cc_final: 0.6919 (mpt) REVERT: B 83 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7195 (mm) REVERT: B 174 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.6921 (p) REVERT: B 183 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 247 GLN cc_start: 0.8166 (mt0) cc_final: 0.7879 (mt0) REVERT: B 256 LYS cc_start: 0.7926 (mttp) cc_final: 0.7664 (mttm) REVERT: B 274 MET cc_start: 0.8034 (mtp) cc_final: 0.7832 (mtp) REVERT: B 283 GLU cc_start: 0.7081 (pm20) cc_final: 0.6735 (mp0) REVERT: B 468 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7293 (ttm170) outliers start: 29 outliers final: 10 residues processed: 139 average time/residue: 0.6901 time to fit residues: 101.5413 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN B 224 ASN B 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115226 restraints weight = 9302.063| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.89 r_work: 0.3105 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8980 Z= 0.117 Angle : 0.526 5.610 12166 Z= 0.272 Chirality : 0.040 0.126 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.645 23.610 1226 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.60 % Allowed : 14.35 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.25), residues: 1112 helix: 0.04 (0.20), residues: 676 sheet: -0.15 (0.56), residues: 82 loop : -1.47 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 463 TYR 0.025 0.001 TYR B 475 PHE 0.021 0.001 PHE B 502 TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS B 662 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8980) covalent geometry : angle 0.52635 (12166) hydrogen bonds : bond 0.03566 ( 446) hydrogen bonds : angle 4.00443 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.403 Fit side-chains REVERT: A 273 GLN cc_start: 0.7706 (mm110) cc_final: 0.7342 (tp40) REVERT: A 346 ASP cc_start: 0.7309 (m-30) cc_final: 0.6921 (m-30) REVERT: A 413 GLN cc_start: 0.8212 (tt0) cc_final: 0.7945 (mt0) REVERT: A 468 ARG cc_start: 0.7703 (ttp80) cc_final: 0.6691 (ttm170) REVERT: A 565 TYR cc_start: 0.8825 (m-80) cc_final: 0.8522 (m-80) REVERT: B 83 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6717 (mm) REVERT: B 174 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6464 (p) REVERT: B 183 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 247 GLN cc_start: 0.7619 (mt0) cc_final: 0.7279 (mt0) REVERT: B 256 LYS cc_start: 0.7519 (mttp) cc_final: 0.7233 (mttm) REVERT: B 283 GLU cc_start: 0.6760 (pm20) cc_final: 0.6343 (mp0) REVERT: B 346 ASP cc_start: 0.7180 (m-30) cc_final: 0.6801 (m-30) REVERT: B 468 ARG cc_start: 0.7596 (ttp80) cc_final: 0.6616 (ttm170) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.7013 time to fit residues: 101.5182 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112828 restraints weight = 9129.707| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.09 r_work: 0.2982 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8980 Z= 0.262 Angle : 0.640 6.074 12166 Z= 0.327 Chirality : 0.047 0.143 1446 Planarity : 0.004 0.044 1494 Dihedral : 4.929 22.628 1225 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.22 % Allowed : 13.72 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.25), residues: 1112 helix: 0.11 (0.20), residues: 666 sheet: -0.25 (0.55), residues: 82 loop : -1.59 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 463 TYR 0.030 0.002 TYR A 475 PHE 0.028 0.002 PHE A 502 TRP 0.010 0.002 TRP A 447 HIS 0.005 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 8980) covalent geometry : angle 0.63978 (12166) hydrogen bonds : bond 0.04790 ( 446) hydrogen bonds : angle 4.25117 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.377 Fit side-chains REVERT: A 83 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7309 (mm) REVERT: A 273 GLN cc_start: 0.8196 (mm110) cc_final: 0.7842 (tp40) REVERT: A 274 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7776 (mtp) REVERT: A 346 ASP cc_start: 0.7581 (m-30) cc_final: 0.7265 (m-30) REVERT: A 468 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7434 (ttm170) REVERT: B 83 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7305 (mm) REVERT: B 174 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7099 (p) REVERT: B 183 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: B 247 GLN cc_start: 0.8255 (mt0) cc_final: 0.7949 (mt0) REVERT: B 256 LYS cc_start: 0.7996 (mttp) cc_final: 0.7755 (mttm) REVERT: B 283 GLU cc_start: 0.7128 (pm20) cc_final: 0.6818 (mp0) REVERT: B 346 ASP cc_start: 0.7527 (m-30) cc_final: 0.7172 (m-30) REVERT: B 468 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7429 (ttm170) REVERT: B 603 MET cc_start: 0.7378 (mpt) cc_final: 0.7138 (mpt) outliers start: 31 outliers final: 15 residues processed: 138 average time/residue: 0.7477 time to fit residues: 108.6103 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN A 413 GLN B 224 ASN B 484 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.158014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114753 restraints weight = 9239.174| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.89 r_work: 0.3077 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8980 Z= 0.119 Angle : 0.532 5.530 12166 Z= 0.273 Chirality : 0.041 0.128 1446 Planarity : 0.004 0.047 1494 Dihedral : 4.588 22.454 1225 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.43 % Allowed : 14.14 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1112 helix: 0.51 (0.20), residues: 668 sheet: -0.23 (0.55), residues: 82 loop : -1.42 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.025 0.001 TYR A 475 PHE 0.024 0.001 PHE A 502 TRP 0.011 0.001 TRP B 447 HIS 0.003 0.001 HIS A 662 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8980) covalent geometry : angle 0.53193 (12166) hydrogen bonds : bond 0.03582 ( 446) hydrogen bonds : angle 3.95725 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.349 Fit side-chains REVERT: A 83 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6719 (mm) REVERT: A 273 GLN cc_start: 0.7694 (mm110) cc_final: 0.7336 (tp40) REVERT: A 346 ASP cc_start: 0.7317 (m-30) cc_final: 0.6960 (m-30) REVERT: A 468 ARG cc_start: 0.7648 (ttp80) cc_final: 0.6651 (ttm170) REVERT: B 83 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6761 (mm) REVERT: B 174 THR cc_start: 0.7020 (OUTLIER) cc_final: 0.6474 (p) REVERT: B 183 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 247 GLN cc_start: 0.7579 (mt0) cc_final: 0.7255 (mt0) REVERT: B 256 LYS cc_start: 0.7493 (mttp) cc_final: 0.7033 (mtpt) REVERT: B 283 GLU cc_start: 0.6835 (pm20) cc_final: 0.6435 (mp0) REVERT: B 346 ASP cc_start: 0.7257 (m-30) cc_final: 0.6830 (m-30) REVERT: B 468 ARG cc_start: 0.7658 (ttp80) cc_final: 0.6671 (ttm170) outliers start: 33 outliers final: 16 residues processed: 133 average time/residue: 0.7026 time to fit residues: 98.8909 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN A 413 GLN B 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114519 restraints weight = 9246.365| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3092 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8980 Z= 0.126 Angle : 0.531 5.516 12166 Z= 0.272 Chirality : 0.041 0.128 1446 Planarity : 0.004 0.043 1494 Dihedral : 4.473 20.873 1225 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.70 % Allowed : 15.59 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1112 helix: 0.64 (0.21), residues: 680 sheet: -0.14 (0.55), residues: 82 loop : -1.34 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 463 TYR 0.023 0.001 TYR B 475 PHE 0.012 0.001 PHE B 499 TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS A 662 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8980) covalent geometry : angle 0.53139 (12166) hydrogen bonds : bond 0.03585 ( 446) hydrogen bonds : angle 3.89194 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.371 Fit side-chains REVERT: A 83 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6784 (mm) REVERT: A 346 ASP cc_start: 0.7349 (m-30) cc_final: 0.6999 (m-30) REVERT: A 468 ARG cc_start: 0.7772 (ttp80) cc_final: 0.6754 (ttm170) REVERT: B 83 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6737 (mm) REVERT: B 174 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6537 (p) REVERT: B 183 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 247 GLN cc_start: 0.7666 (mt0) cc_final: 0.7358 (mt0) REVERT: B 256 LYS cc_start: 0.7508 (mttp) cc_final: 0.7063 (mtpt) REVERT: B 283 GLU cc_start: 0.6885 (pm20) cc_final: 0.6494 (mp0) REVERT: B 346 ASP cc_start: 0.7280 (m-30) cc_final: 0.6739 (m-30) REVERT: B 468 ARG cc_start: 0.7774 (ttp80) cc_final: 0.6770 (ttm170) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 0.6632 time to fit residues: 88.8138 Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 266 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116106 restraints weight = 9143.679| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.90 r_work: 0.3115 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8980 Z= 0.105 Angle : 0.507 5.487 12166 Z= 0.258 Chirality : 0.040 0.129 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.298 20.235 1225 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.60 % Allowed : 16.53 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.26), residues: 1112 helix: 0.94 (0.21), residues: 674 sheet: -0.09 (0.54), residues: 84 loop : -1.30 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.021 0.001 TYR A 475 PHE 0.025 0.001 PHE A 502 TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8980) covalent geometry : angle 0.50704 (12166) hydrogen bonds : bond 0.03262 ( 446) hydrogen bonds : angle 3.75917 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.331 Fit side-chains REVERT: A 174 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6575 (p) REVERT: A 346 ASP cc_start: 0.7231 (m-30) cc_final: 0.6665 (m-30) REVERT: A 468 ARG cc_start: 0.7776 (ttp80) cc_final: 0.6725 (ttm170) REVERT: B 174 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6541 (p) REVERT: B 183 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: B 247 GLN cc_start: 0.7650 (mt0) cc_final: 0.7343 (mt0) REVERT: B 256 LYS cc_start: 0.7531 (mttp) cc_final: 0.7079 (mtpt) REVERT: B 283 GLU cc_start: 0.6739 (pm20) cc_final: 0.6437 (mp0) REVERT: B 314 ASP cc_start: 0.7042 (m-30) cc_final: 0.6488 (m-30) REVERT: B 346 ASP cc_start: 0.7200 (m-30) cc_final: 0.6653 (m-30) REVERT: B 468 ARG cc_start: 0.7733 (ttp80) cc_final: 0.6731 (ttm170) outliers start: 25 outliers final: 13 residues processed: 129 average time/residue: 0.6332 time to fit residues: 86.7571 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 0.0470 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 266 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112137 restraints weight = 9252.099| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.80 r_work: 0.3111 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8980 Z= 0.099 Angle : 0.501 6.739 12166 Z= 0.255 Chirality : 0.040 0.130 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.153 18.760 1224 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.39 % Allowed : 17.46 % Favored : 80.15 % 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 aren not related in a simple way. whole: 0.43 (0.26), residues: 1112 helix: 1.15 (0.21), residues: 674 sheet: -0.09 (0.54), residues: 84 loop : -1.27 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 463 TYR 0.021 0.001 TYR A 475 PHE 0.012 0.001 PHE B 499 TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8980) covalent geometry : angle 0.50086 (12166) hydrogen bonds : bond 0.03141 ( 446) hydrogen bonds : angle 3.65654 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.347 Fit side-chains REVERT: A 83 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6717 (mm) REVERT: A 174 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6463 (p) REVERT: A 346 ASP cc_start: 0.7188 (m-30) cc_final: 0.6622 (m-30) REVERT: A 468 ARG cc_start: 0.7553 (ttp80) cc_final: 0.6581 (ttm170) REVERT: B 83 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6716 (mm) REVERT: B 174 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6436 (p) REVERT: B 183 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: B 247 GLN cc_start: 0.7532 (mt0) cc_final: 0.7188 (mt0) REVERT: B 256 LYS cc_start: 0.7446 (mttp) cc_final: 0.6988 (mtpt) REVERT: B 283 GLU cc_start: 0.6686 (pm20) cc_final: 0.6365 (mp0) REVERT: B 314 ASP cc_start: 0.6908 (m-30) cc_final: 0.6368 (m-30) REVERT: B 346 ASP cc_start: 0.7226 (m-30) cc_final: 0.6635 (m-30) REVERT: B 468 ARG cc_start: 0.7543 (ttp80) cc_final: 0.6592 (ttm170) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 0.6090 time to fit residues: 84.0523 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109946 restraints weight = 9250.048| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.81 r_work: 0.3092 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8980 Z= 0.132 Angle : 0.531 6.006 12166 Z= 0.269 Chirality : 0.041 0.129 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.288 18.461 1224 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.87 % Allowed : 17.98 % Favored : 80.15 % 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 aren not related in a simple way. whole: 0.35 (0.26), residues: 1112 helix: 1.08 (0.21), residues: 676 sheet: -0.14 (0.54), residues: 82 loop : -1.29 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 463 TYR 0.022 0.001 TYR A 475 PHE 0.029 0.001 PHE A 502 TRP 0.009 0.001 TRP A 447 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8980) covalent geometry : angle 0.53093 (12166) hydrogen bonds : bond 0.03574 ( 446) hydrogen bonds : angle 3.77147 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.353 Fit side-chains REVERT: A 174 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6468 (p) REVERT: A 346 ASP cc_start: 0.7167 (m-30) cc_final: 0.6594 (m-30) REVERT: A 468 ARG cc_start: 0.7644 (ttp80) cc_final: 0.6595 (ttm170) REVERT: B 174 THR cc_start: 0.6992 (OUTLIER) cc_final: 0.6464 (p) REVERT: B 183 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: B 247 GLN cc_start: 0.7487 (mt0) cc_final: 0.7115 (mt0) REVERT: B 256 LYS cc_start: 0.7441 (mttp) cc_final: 0.6968 (mtpt) REVERT: B 283 GLU cc_start: 0.6666 (pm20) cc_final: 0.6345 (mp0) REVERT: B 346 ASP cc_start: 0.7199 (m-30) cc_final: 0.6629 (m-30) REVERT: B 468 ARG cc_start: 0.7601 (ttp80) cc_final: 0.6598 (ttm170) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.6571 time to fit residues: 86.3382 Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111947 restraints weight = 9174.413| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.80 r_work: 0.3122 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8980 Z= 0.105 Angle : 0.505 5.875 12166 Z= 0.257 Chirality : 0.040 0.132 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.155 17.522 1224 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 17.98 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1112 helix: 1.27 (0.21), residues: 672 sheet: -0.03 (0.54), residues: 84 loop : -1.27 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.021 0.001 TYR A 475 PHE 0.012 0.001 PHE B 499 TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8980) covalent geometry : angle 0.50471 (12166) hydrogen bonds : bond 0.03230 ( 446) hydrogen bonds : angle 3.65892 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3447.91 seconds wall clock time: 59 minutes 37.00 seconds (3577.00 seconds total)