Starting phenix.real_space_refine on Sat Jun 7 13:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3d_35150/06_2025/8i3d_35150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3d_35150/06_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_35150/06_2025/8i3d_35150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3d_35150/06_2025/8i3d_35150.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3d_35150/06_2025/8i3d_35150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3d_35150/06_2025/8i3d_35150.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.107 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.56, per 1000 atoms: 0.97 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.14 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: 2.69 Time building geometry restraints manager: 2.68 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: 0.05 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: 2.820 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.160 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.003 TRP A 425 HIS 0.009 0.002 HIS A 662 PHE 0.021 0.002 PHE A 499 TYR 0.037 0.002 TYR A 475 ARG 0.006 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.29637 ( 446) hydrogen bonds : angle 10.05893 ( 1302) covalent geometry : bond 0.00931 ( 8980) covalent geometry : angle 0.99324 (12166) *********************** 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 : 1.013 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: 1.5364 time to fit residues: 273.5337 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 : 0.864 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.157277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115568 restraints weight = 9046.019| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.73 r_work: 0.3040 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1715 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= 0.122 Angle : 0.576 5.858 12166 Z= 0.303 Chirality : 0.040 0.127 1446 Planarity : 0.006 0.045 1494 Dihedral : 5.231 39.642 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.22 % Allowed : 10.60 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.21), residues: 1112 helix: -1.99 (0.16), residues: 676 sheet: -0.34 (0.57), residues: 82 loop : -1.94 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS A 434 PHE 0.009 0.001 PHE A 502 TYR 0.028 0.001 TYR A 475 ARG 0.010 0.001 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 446) hydrogen bonds : angle 4.67861 ( 1302) covalent geometry : bond 0.00263 ( 8980) covalent geometry : angle 0.57603 (12166) *********************** 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 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.920 Fit side-chains REVERT: A 273 GLN cc_start: 0.8152 (mm110) cc_final: 0.7803 (tp40) REVERT: A 274 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7622 (mtp) REVERT: A 346 ASP cc_start: 0.7331 (m-30) cc_final: 0.7081 (m-30) REVERT: A 413 GLN cc_start: 0.8523 (tt0) cc_final: 0.8272 (mt0) REVERT: A 468 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7292 (ttm170) REVERT: B 174 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.6844 (p) REVERT: B 183 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 247 GLN cc_start: 0.8211 (mt0) cc_final: 0.7959 (mt0) REVERT: B 256 LYS cc_start: 0.7993 (mttp) cc_final: 0.7739 (mttm) REVERT: B 283 GLU cc_start: 0.6945 (pm20) cc_final: 0.6498 (mp0) REVERT: B 326 THR cc_start: 0.5893 (OUTLIER) cc_final: 0.5691 (t) REVERT: B 468 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7168 (ttm170) outliers start: 31 outliers final: 6 residues processed: 156 average time/residue: 1.5204 time to fit residues: 250.6785 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 326 THR 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 68 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 154 HIS B 224 ASN B 266 GLN B 531 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111467 restraints weight = 9190.627| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.91 r_work: 0.2969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8980 Z= 0.177 Angle : 0.592 5.753 12166 Z= 0.305 Chirality : 0.043 0.135 1446 Planarity : 0.005 0.048 1494 Dihedral : 4.976 24.427 1227 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.01 % Allowed : 12.58 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1112 helix: -0.60 (0.19), residues: 678 sheet: -0.13 (0.57), residues: 82 loop : -1.76 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 447 HIS 0.005 0.001 HIS B 662 PHE 0.021 0.002 PHE B 502 TYR 0.028 0.002 TYR A 475 ARG 0.010 0.001 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 446) hydrogen bonds : angle 4.29935 ( 1302) covalent geometry : bond 0.00427 ( 8980) covalent geometry : angle 0.59244 (12166) *********************** 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 : 0.919 Fit side-chains REVERT: A 83 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7157 (mm) REVERT: A 273 GLN cc_start: 0.8035 (mm110) cc_final: 0.7665 (tp40) REVERT: A 274 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7630 (mtp) REVERT: A 346 ASP cc_start: 0.7331 (m-30) cc_final: 0.6982 (m-30) REVERT: A 413 GLN cc_start: 0.8476 (tt0) cc_final: 0.8251 (mt0) REVERT: A 468 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7192 (ttm170) REVERT: B 83 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7133 (mm) REVERT: B 174 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.6780 (p) REVERT: B 183 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 247 GLN cc_start: 0.8081 (mt0) cc_final: 0.7800 (mt0) REVERT: B 256 LYS cc_start: 0.7865 (mttp) cc_final: 0.7587 (mttm) REVERT: B 283 GLU cc_start: 0.6979 (pm20) cc_final: 0.6604 (mp0) REVERT: B 468 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7173 (ttm170) outliers start: 29 outliers final: 10 residues processed: 139 average time/residue: 1.8978 time to fit residues: 279.3473 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 45 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 224 ASN B 266 GLN B 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115359 restraints weight = 9026.618| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.94 r_work: 0.2975 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8980 Z= 0.167 Angle : 0.569 5.631 12166 Z= 0.293 Chirality : 0.042 0.133 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.794 24.004 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.33 % Allowed : 14.03 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1112 helix: -0.07 (0.20), residues: 678 sheet: -0.15 (0.56), residues: 82 loop : -1.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 447 HIS 0.004 0.001 HIS B 662 PHE 0.023 0.002 PHE A 502 TYR 0.027 0.001 TYR B 475 ARG 0.008 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 446) hydrogen bonds : angle 4.13185 ( 1302) covalent geometry : bond 0.00404 ( 8980) covalent geometry : angle 0.56884 (12166) *********************** 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 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.851 Fit side-chains REVERT: A 83 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7148 (mm) REVERT: A 273 GLN cc_start: 0.8080 (mm110) cc_final: 0.7721 (tp40) REVERT: A 274 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7588 (mtp) REVERT: A 346 ASP cc_start: 0.7507 (m-30) cc_final: 0.7151 (m-30) REVERT: A 468 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7268 (ttm170) REVERT: A 603 MET cc_start: 0.7443 (mpt) cc_final: 0.7162 (mpt) REVERT: B 83 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7120 (mm) REVERT: B 174 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.6917 (p) REVERT: B 183 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 247 GLN cc_start: 0.8137 (mt0) cc_final: 0.7832 (mt0) REVERT: B 256 LYS cc_start: 0.7920 (mttp) cc_final: 0.7660 (mttm) REVERT: B 283 GLU cc_start: 0.7071 (pm20) cc_final: 0.6727 (mp0) REVERT: B 346 ASP cc_start: 0.7466 (m-30) cc_final: 0.7137 (m-30) REVERT: B 468 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7240 (ttm170) REVERT: B 603 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6989 (mpt) outliers start: 32 outliers final: 12 residues processed: 138 average time/residue: 1.4882 time to fit residues: 217.0691 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 238 ASP 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 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 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 603 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 484 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113974 restraints weight = 9077.502| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.98 r_work: 0.2955 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8980 Z= 0.191 Angle : 0.588 5.653 12166 Z= 0.302 Chirality : 0.044 0.136 1446 Planarity : 0.004 0.048 1494 Dihedral : 4.823 22.541 1226 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.12 % Allowed : 14.55 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1112 helix: 0.21 (0.20), residues: 668 sheet: -0.20 (0.55), residues: 82 loop : -1.50 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.007 0.001 HIS B 662 PHE 0.026 0.002 PHE A 502 TYR 0.028 0.002 TYR B 475 ARG 0.009 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 446) hydrogen bonds : angle 4.12977 ( 1302) covalent geometry : bond 0.00467 ( 8980) covalent geometry : angle 0.58825 (12166) *********************** 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 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.827 Fit side-chains REVERT: A 83 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7211 (mm) REVERT: A 273 GLN cc_start: 0.8057 (mm110) cc_final: 0.7702 (tp40) REVERT: A 274 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: A 346 ASP cc_start: 0.7499 (m-30) cc_final: 0.7151 (m-30) REVERT: A 468 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7272 (ttm170) REVERT: B 83 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7143 (mm) REVERT: B 174 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.6963 (p) REVERT: B 183 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: B 247 GLN cc_start: 0.8130 (mt0) cc_final: 0.7790 (mt0) REVERT: B 256 LYS cc_start: 0.7906 (mttp) cc_final: 0.7656 (mttm) REVERT: B 283 GLU cc_start: 0.7085 (pm20) cc_final: 0.6730 (mp0) REVERT: B 346 ASP cc_start: 0.7507 (m-30) cc_final: 0.7190 (m-30) REVERT: B 468 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7269 (ttm170) REVERT: B 603 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7011 (mpt) outliers start: 30 outliers final: 15 residues processed: 139 average time/residue: 1.3609 time to fit residues: 200.2912 Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 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 238 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 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 Chi-restraints excluded: chain B residue 603 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.157300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113854 restraints weight = 9113.319| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.89 r_work: 0.3049 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8980 Z= 0.146 Angle : 0.545 5.561 12166 Z= 0.280 Chirality : 0.042 0.129 1446 Planarity : 0.004 0.043 1494 Dihedral : 4.647 22.180 1226 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.74 % Allowed : 14.03 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1112 helix: 0.51 (0.20), residues: 668 sheet: -0.19 (0.55), residues: 82 loop : -1.44 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 447 HIS 0.003 0.001 HIS B 662 PHE 0.028 0.002 PHE A 502 TYR 0.025 0.001 TYR B 475 ARG 0.008 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 446) hydrogen bonds : angle 3.98718 ( 1302) covalent geometry : bond 0.00349 ( 8980) covalent geometry : angle 0.54543 (12166) *********************** 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 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.971 Fit side-chains REVERT: A 83 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6708 (mm) REVERT: A 273 GLN cc_start: 0.7703 (mm110) cc_final: 0.7348 (tp40) REVERT: A 274 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: A 346 ASP cc_start: 0.7303 (m-30) cc_final: 0.6950 (m-30) REVERT: A 468 ARG cc_start: 0.7625 (ttp80) cc_final: 0.6623 (ttm170) REVERT: B 83 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6742 (mm) REVERT: B 174 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6501 (p) REVERT: B 183 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: B 247 GLN cc_start: 0.7603 (mt0) cc_final: 0.7303 (mt0) REVERT: B 256 LYS cc_start: 0.7492 (mttp) cc_final: 0.7019 (mtpt) REVERT: B 283 GLU cc_start: 0.6849 (pm20) cc_final: 0.6448 (mp0) REVERT: B 346 ASP cc_start: 0.7266 (m-30) cc_final: 0.6752 (m-30) REVERT: B 468 ARG cc_start: 0.7680 (ttp80) cc_final: 0.6686 (ttm170) outliers start: 36 outliers final: 18 residues processed: 139 average time/residue: 1.3610 time to fit residues: 200.6407 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 274 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 83 ILE 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 238 ASP 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 68 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.159032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115651 restraints weight = 9241.089| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.90 r_work: 0.3110 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2482 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= 0.111 Angle : 0.517 5.506 12166 Z= 0.265 Chirality : 0.040 0.128 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.427 20.527 1226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.81 % Allowed : 15.18 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1112 helix: 0.75 (0.21), residues: 676 sheet: -0.15 (0.55), residues: 82 loop : -1.31 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS B 662 PHE 0.012 0.001 PHE B 499 TYR 0.023 0.001 TYR A 475 ARG 0.006 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 446) hydrogen bonds : angle 3.84156 ( 1302) covalent geometry : bond 0.00255 ( 8980) covalent geometry : angle 0.51745 (12166) *********************** 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 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.947 Fit side-chains REVERT: A 346 ASP cc_start: 0.7251 (m-30) cc_final: 0.6832 (m-30) REVERT: A 468 ARG cc_start: 0.7751 (ttp80) cc_final: 0.6730 (ttm170) REVERT: B 174 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6560 (p) REVERT: B 183 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: B 247 GLN cc_start: 0.7648 (mt0) cc_final: 0.7348 (mt0) REVERT: B 256 LYS cc_start: 0.7522 (mttp) cc_final: 0.7076 (mtpt) REVERT: B 283 GLU cc_start: 0.6835 (pm20) cc_final: 0.6441 (mp0) REVERT: B 346 ASP cc_start: 0.7208 (m-30) cc_final: 0.6671 (m-30) REVERT: B 468 ARG cc_start: 0.7771 (ttp80) cc_final: 0.6738 (ttm170) outliers start: 27 outliers final: 14 residues processed: 127 average time/residue: 1.3438 time to fit residues: 182.2579 Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 133 LYS 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 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 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 90 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.159409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115847 restraints weight = 9230.084| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.93 r_work: 0.3107 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8980 Z= 0.110 Angle : 0.512 5.823 12166 Z= 0.261 Chirality : 0.040 0.127 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.331 20.316 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.81 % Allowed : 16.42 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1112 helix: 0.94 (0.21), residues: 674 sheet: -0.14 (0.54), residues: 84 loop : -1.28 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS B 154 PHE 0.025 0.001 PHE A 502 TYR 0.022 0.001 TYR B 475 ARG 0.007 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 446) hydrogen bonds : angle 3.76866 ( 1302) covalent geometry : bond 0.00250 ( 8980) covalent geometry : angle 0.51206 (12166) *********************** 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 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.914 Fit side-chains REVERT: A 174 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6578 (p) REVERT: A 346 ASP cc_start: 0.7233 (m-30) cc_final: 0.6650 (m-30) REVERT: A 468 ARG cc_start: 0.7784 (ttp80) cc_final: 0.6736 (ttm170) REVERT: B 83 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6778 (mm) REVERT: B 174 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6564 (p) REVERT: B 183 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 247 GLN cc_start: 0.7671 (mt0) cc_final: 0.7327 (mt0) REVERT: B 256 LYS cc_start: 0.7559 (mttp) cc_final: 0.7078 (mtpt) REVERT: B 283 GLU cc_start: 0.6807 (pm20) cc_final: 0.6507 (mp0) REVERT: B 346 ASP cc_start: 0.7257 (m-30) cc_final: 0.6720 (m-30) REVERT: B 468 ARG cc_start: 0.7818 (ttp80) cc_final: 0.6760 (ttm170) outliers start: 27 outliers final: 15 residues processed: 132 average time/residue: 1.2136 time to fit residues: 170.8975 Evaluate side-chains 122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 133 LYS 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 238 ASP 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 11 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 108 optimal weight: 0.6980 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.158301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114606 restraints weight = 9301.869| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.94 r_work: 0.3088 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8980 Z= 0.137 Angle : 0.536 6.449 12166 Z= 0.274 Chirality : 0.041 0.129 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.406 19.705 1226 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 16.94 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1112 helix: 0.89 (0.21), residues: 680 sheet: -0.16 (0.54), residues: 82 loop : -1.26 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS B 154 PHE 0.011 0.001 PHE A 499 TYR 0.023 0.001 TYR A 475 ARG 0.008 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 446) hydrogen bonds : angle 3.82398 ( 1302) covalent geometry : bond 0.00325 ( 8980) covalent geometry : angle 0.53591 (12166) *********************** 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 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.978 Fit side-chains REVERT: A 174 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6597 (p) REVERT: A 346 ASP cc_start: 0.7216 (m-30) cc_final: 0.6614 (m-30) REVERT: A 468 ARG cc_start: 0.7789 (ttp80) cc_final: 0.6741 (ttm170) REVERT: B 83 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6790 (mm) REVERT: B 174 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6585 (p) REVERT: B 183 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: B 247 GLN cc_start: 0.7649 (mt0) cc_final: 0.7279 (mt0) REVERT: B 256 LYS cc_start: 0.7557 (mttp) cc_final: 0.7066 (mtpt) REVERT: B 283 GLU cc_start: 0.6772 (pm20) cc_final: 0.6457 (mp0) REVERT: B 346 ASP cc_start: 0.7257 (m-30) cc_final: 0.6699 (m-30) REVERT: B 468 ARG cc_start: 0.7799 (ttp80) cc_final: 0.6759 (ttm170) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 1.3432 time to fit residues: 178.4542 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.160061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116350 restraints weight = 9228.823| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.92 r_work: 0.3105 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8980 Z= 0.108 Angle : 0.508 6.116 12166 Z= 0.259 Chirality : 0.040 0.130 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.262 18.860 1226 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1112 helix: 1.11 (0.21), residues: 674 sheet: -0.08 (0.53), residues: 84 loop : -1.26 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 154 PHE 0.028 0.001 PHE A 502 TYR 0.021 0.001 TYR A 475 ARG 0.007 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 446) hydrogen bonds : angle 3.70751 ( 1302) covalent geometry : bond 0.00247 ( 8980) covalent geometry : angle 0.50766 (12166) ********************** 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 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.964 Fit side-chains REVERT: A 174 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6556 (p) REVERT: A 346 ASP cc_start: 0.7244 (m-30) cc_final: 0.6654 (m-30) REVERT: A 468 ARG cc_start: 0.7680 (ttp80) cc_final: 0.6664 (ttm170) REVERT: B 83 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6722 (mm) REVERT: B 174 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6570 (p) REVERT: B 183 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: B 247 GLN cc_start: 0.7576 (mt0) cc_final: 0.7217 (mt0) REVERT: B 256 LYS cc_start: 0.7527 (mttp) cc_final: 0.7041 (mtpt) REVERT: B 283 GLU cc_start: 0.6708 (pm20) cc_final: 0.6398 (mp0) REVERT: B 346 ASP cc_start: 0.7257 (m-30) cc_final: 0.6693 (m-30) REVERT: B 468 ARG cc_start: 0.7717 (ttp80) cc_final: 0.6712 (ttm170) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 1.3055 time to fit residues: 178.2852 Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 A residue 660 ILE Chi-restraints excluded: chain B residue 83 ILE 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 282 SER 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 29 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.153883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113062 restraints weight = 9197.933| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.25 r_work: 0.2917 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8980 Z= 0.222 Angle : 0.611 5.808 12166 Z= 0.311 Chirality : 0.046 0.137 1446 Planarity : 0.004 0.048 1494 Dihedral : 4.644 19.144 1224 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.49 % Allowed : 17.98 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1112 helix: 0.81 (0.20), residues: 668 sheet: -0.18 (0.54), residues: 82 loop : -1.39 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 636 HIS 0.005 0.001 HIS A 395 PHE 0.016 0.002 PHE B 387 TYR 0.027 0.002 TYR B 475 ARG 0.011 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 446) hydrogen bonds : angle 4.05546 ( 1302) covalent geometry : bond 0.00547 ( 8980) covalent geometry : angle 0.61132 (12166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7188.18 seconds wall clock time: 125 minutes 21.83 seconds (7521.83 seconds total)